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Single Polymorphism Nucleotide (SNPs)

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https://www.readbyqxmd.com/read/29792983/impact-of-genetic-influence-on-serum-total-and-free-25-hydroxyvitamin-d-in-humans
#1
Balázs Szili, Boglárka Szabó, Péter Horváth, Bence Bakos, Györgyi Kirschner, János P Kósa, Erzsébet Toldy, Zsuzsanna Putz, Péter Lakatos, Ádám Tabák, István Takács
Serum 25-hydroxyvitamin D /25OHD/ levels in humans are determined primarily by environmental factors such as UV-B radiation and diet, including vitamin D intake. Although some genetic determinants of 25OHD levels have been shown, the magnitude of this association has not yet been clarified. The present study evaluates the genetic contribution to total- /t-25OHD/ and free-25OHD /f-25OHD/ in a representative sample of the Hungarian population (n = 462). The study was performed at the end of winter to minimize the effect of sunlight, which is a major determinant of serum vitamin D levels...
May 21, 2018: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29792895/pharmacogenomics-of-drug-induced-liver-injury-dili-molecular-biology-to-clinical-applications
#2
REVIEW
Kalaiyarasi Kaliyaperumal, Jane I Grove, Robin M Delahay, William J H Griffiths, Adam Duckworth, Guruprasad P Aithal
A number of drug-specific and host-related factors contribute to the development of drug-induced liver injury (DILI). Investigations focused on genetic susceptibility to DILI have advanced our understanding of the pathogenesis of this rare, yet potentially life-threatening adverse reaction. Candidate gene studies involving well-characterized patients with DILI and drug-exposed controls have identified single nucleotide polymorphisms (SNPs) affecting the metabolism and clearance of specific drugs and hence, influencing individual's susceptibility to DILI...
May 21, 2018: Journal of Hepatology
https://www.readbyqxmd.com/read/29792870/peripheral-complement-interactions-with-amyloid-%C3%AE-peptide-in-alzheimer-s-disease-polymorphisms-structure-and-function-of-complement-receptor-1
#3
Jenny U Johansson, William D Brubaker, Harold Javitz, Andrew W Bergen, Denise Nishita, Abhishek Trigunaite, Andrés Crane, Justine Ceballos, Diego Mastroeni, Andrea J Tenner, Marwan Sabbagh, Joseph Rogers
INTRODUCTION: Genome-wide association studies consistently show that single nucleotide polymorphisms (SNPs) in the complement receptor 1 (CR1) gene modestly but significantly alter Alzheimer's disease (AD) risk. Follow-up research has assumed that CR1 is expressed in the human brain despite a paucity of evidence for its function there. Alternatively, erythrocytes contain >80% of the body's CR1, where, in primates, it is known to bind circulating pathogens. METHODS: Multidisciplinary methods were employed...
May 21, 2018: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/29792121/abcg2-polymorphism-rs2231142-and-hypothyroidism-in-metastatic-renal-cell-carcinoma-patients-treated-with-sunitinib
#4
Emilie Werbrouck, Julie Bastin, Diether Lambrechts, Annelies Verbiest, Thomas Van Brussel, Evelyne Lerut, Jean-Pascal Machiels, Vincent Verschaeve, Vincent Richard, Philip R Debruyne, Brigitte Decallonne, Patrick Schöffski, Oliver Bechter, Pascal Wolter, Benoit Beuselinck
Background and aim Vascular endothelial growth factor receptor tyrosine kinase inhibitors (VEGFR-TKIs) cause significant adverse events including thyroid dysfunction, mainly hypothyroidism, in a considerable proportion of patients. In a series of metastatic renal cell carcinoma (mRCC) patients treated with sunitinib, we aimed to study the correlation between hypothyroidism and single nucleotide polymorphisms (SNPs) in genes involved in sunitinib pharmacokinetics and pharmacodynamics. Patients and methods We included 79 mRCC patients who started sunitinib between November 2005 and March 2016...
May 23, 2018: Acta Clinica Belgica
https://www.readbyqxmd.com/read/29791011/a-pharmacokinetic-and-pharmacogenetic-analysis-of-osteosarcoma-patients-treated-with-high-dose-methotrexate-data-from-the-os2006-sarcoma-09-trial
#5
Gabrielle Lui, Jean-Marc Treluyer, Brice Fresneau, Sophie Piperno-Neumann, Nathalie Gaspar, Nadège Corradini, Jean-Claude Gentet, Perrine Marec Berard, Valérie Laurence, Pascale Schneider, Natacha Entz-Werle, Hélène Pacquement, Frédéric Millot, Sophie Taque, Claire Freycon, Cyril Lervat, Marie Cécile Le Deley, Céline Mahier Ait Oukhatar, Laurence Brugieres, Gwénaël Le Teuff, Naïm Bouazza
Growing evidence suggests that polymorphisms of genes coding for transporters or enzymes may partially explain the large between subject variability reported for methotrexate (MTX) pharmacokinetics (PK). This prospective study aimed to develop a population PK-pharmacogenetic model to evaluate the part of between-subject variability due to single-nucleotide polymorphisms (SNPs) in transporters and enzyme genes implicated in MTX distribution and elimination. MTX concentrations and 54 SNPs (located in ABCB1, ABCC1, ABCC2, ABCC3, ABCC4, ABCG2, SLC19A1, SLCO1B1, and UGT1A1 genes) were analyzed in patients treated with MTX included in the OS2006/sarcoma-09 trial (a multicenter, open-label, phase III trial, ClinicalTrials...
May 23, 2018: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29789989/influence-of-tissue-factor-polymorphisms-603a-g-and-5466a-g-on-plasma-tissue-factor-levels-and-their-impact-on-deep-vein-thrombosis-risk-in-young-indian-population
#6
Kamal Kishor, Amit Sharma, Kanwaljeet Singh, Ravi Ranjan, Hareram Pandey, Ravi Kumar, Vineet Kumar Kamal, Pravas Mishra, Manoranjan Mahapatra, Renu Saxena
Deep vein thrombosis (DVT) is multifactorial disorder and well known to cause substantial morbidity and mortality. There is sparse data in the Asian population, particularly India regarding association of tissue factor (TF) gene single nucleotide polymorphisms (SNPs) with plasma TF levels in DVT. So, we analyzed the distribution of SNPs (603A>G and 5466A>G) in India, to evaluate their effect on TF levels in DVT patients. Plasma level and SNPs (603A>G and 5466A>G) of TF gene were screened in subjects (100 DVT patients and 100 controls)...
May 22, 2018: Journal of Thrombosis and Thrombolysis
https://www.readbyqxmd.com/read/29789573/high-throughput-screening-of-prostate-cancer-risk-loci-by-single-nucleotide-polymorphisms-sequencing
#7
Peng Zhang, Ji-Han Xia, Jing Zhu, Ping Gao, Yi-Jun Tian, Meijun Du, Yong-Chen Guo, Sufyan Suleman, Qin Zhang, Manish Kohli, Lori S Tillmans, Stephen N Thibodeau, Amy J French, James R Cerhan, Li-Dong Wang, Gong-Hong Wei, Liang Wang
Functional characterization of disease-causing variants at risk loci has been a significant challenge. Here we report a high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) technology to simultaneously screen hundreds to thousands of SNPs for their allele-dependent protein-binding differences. This technology takes advantage of higher retention rate of protein-bound DNA oligos in protein purification column to quantitatively sequence these SNP-containing oligos. We apply this technology to test prostate cancer-risk loci and observe differential allelic protein binding in a significant number of selected SNPs...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789205/genetic-variants-related-to-urate-and-risk-of-parkinson-s-disease
#8
Katherine C Hughes, Xiang Gao, Eilis J O'Reilly, Iris Y Kim, Molin Wang, Marc G Weisskopf, Michael A Schwarzschild, Alberto Ascherio
INTRODUCTION: Higher urate concentrations have been associated with a lower risk of developing Parkinson's disease (PD) and with slower rates of clinical decline in PD patients. Whether these associations reflect a neuroprotective effect of urate is unclear. Our objective was to assess whether genetic variants that modify circulating urate levels are also associated with altered PD risk. METHODS: Participants were from three large ongoing cohort studies: the Nurses' Health Study (NHS), the Health Professionals Follow-up Study (HPFS), and the Cancer Prevention Study II Nutrition Cohort (CPS-IIN)...
May 1, 2018: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29788905/genomic-prediction-of-the-polled-and-horned-phenotypes-in-merino-sheep
#9
Naomi Duijvesteijn, Sunduimijid Bolormaa, Hans D Daetwyler, Julius H J van der Werf
BACKGROUND: In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polled, scurs, knobs or horns. Derived phenotypes polled/non-polled (P/NP) and horned/non-horned (H/NH) were used to test four different strategies for prediction in 4001 purebred Merino sheep. These strategies include the use of single 'single nucleotide polymorphism' (SNP) genotypes, multiple-SNP haplotypes, genome-wide and chromosome-wide genomic best linear unbiased prediction and information from imputed sequence variants from the region including the RXFP2 gene...
May 22, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29788182/global-distribution-of-genetic-traits-gadget-web-server-polygenic-trait-scores-worldwide
#10
Aroon T Chande, Lu Wang, Lavanya Rishishwar, Andrew B Conley, Emily T Norris, Augusto Valderrama-Aguirre, I King Jordan
Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29787827/genetic-variants-of-fatty-acid-elongase-6-in-chinese-holstein-cow
#11
Si Chen, Menglin Chai, Chen Tian, Yuzhuang Li, Tian Deng, Hui Wu, Xiaolin Liu
In the dairy industry, genetic variants have contributed to the improvement of milk production traits. Fatty acid elongase 6 (ELOVL6), which elongates saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs), plays a distinct role in the balance of long-chain fatty acids composition in animals. ELOVL6 catalyzes the elongation of palmitic acids (C16:0) which is the most common saturated fatty acid found in animals and also an essential precursor to synthesize other long-chain fatty acids. However, the genetic variant research of bovine ELOVL6 on milk quality traits is still unknown...
May 19, 2018: Gene
https://www.readbyqxmd.com/read/29787601/impact-of-vascular-endothelial-growth-factor-vegf-and-vascular-endothelial-growth-factor-receptor-vegfr-single-nucleotide-polymorphisms-on-outcome-in-gastroenteropancreatic-neuroendocrine-neoplasms
#12
Rossana Berardi, Mariangela Torniai, Stefano Partelli, Corrado Rubini, Silvia Pagliaretta, Agnese Savini, Vanessa Polenta, Matteo Santoni, Riccardo Giampieri, Sofia Onorati, Federica Barucca, Alberto Murrone, Francesca Bianchi, Massimo Falconi
Angiogenesis represents a key event in cancer development, leading to local invasion e metastatization, and might be considered a basic feature in gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) with a high expression of angiogenic molecules. We aimed to analyze the prognostic and predictive role of angiogenic factors in GEP-NENs through the analysis of single nucleotide polymorphisms (SNPs) of VEGF-A, VEGFR2 and VEGFR3. The genomic DNA of 58 consecutive patients with GEP-NENs treated at our Institution was extracted from peripheral blood...
2018: PloS One
https://www.readbyqxmd.com/read/29786918/novel-genes-and-insights-in-complete-asthma-remission
#13
Judith M Vonk, Maartje A E Nieuwenhuis, F Nicole Dijk, Anne Boudier, Valerie Siroux, Emmanuelle Bouzigon, Nicole Probst-Hensch, Medea Imboden, Dirk Keidel, Don Sin, Yohan Bossé, Ke Hao, Maarten van den Berge, Alen Faiz, Gerard H Koppelman, Dirkje S Postma
BACKGROUND: Asthma is a chronic respiratory disease without a cure, though there exists spontaneous remission. Genome wide association(GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVES: We performed a GWA study to develop insights in asthma remission. METHODS: Clinical remission (ClinR) was defined by absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years, and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR)...
May 22, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29785906/molecular-characterisation-of-the-buffalo-scap-gene-and-its-association-with-milk-production-traits-in-water-buffaloes
#14
Tingxian Deng, Xiaoya Ma, Chunying Pang, Shasha Liang, Xingrong Lu, Anqin Duan, Xianwei Liang
The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffalo SCAP gene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed the SCAP gene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile of SCAP gene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffalo SCAP gene were identified, six of them (g...
May 2018: Journal of Dairy Research
https://www.readbyqxmd.com/read/29785637/frzb1-rs2242070-polymorphisms-is-associated-with-brick-tea-type-skeletal-fluorosis-in-kazakhs-but-not-in-tibetans-china
#15
Yanmei Yang, Qiaoshi Zhao, Yang Liu, Xiaona Liu, Yanru Chu, Huazhu Yan, Yumei Fan, Simeng Huo, Limei Wang, Qun Lou, Ning Guo, Dianjun Sun, Yanhui Gao
Skeletal fluorosis is a metabolic bone and joint disease caused by excessive accumulation of fluoride in the bones. Compared with Kazakhs, Tibetans are more likely to develop moderate and severe brick tea type skeletal fluorosis, although they have similar fluoride exposure. Single nucleotide polymorphisms (SNPs) in frizzled-related protein (FRZB) have been associated with osteoarthritis, but their association with the risk of skeletal fluorosis has not been reported. In this paper, we investigated the association of three SNPs (rs7775, rs2242070 and rs9288087) in FRZB1with brick tea type skeletal fluorosis risk in a cross-sectional case-control study conducted in Sinkiang and Qinghai, China...
May 21, 2018: Archives of Toxicology
https://www.readbyqxmd.com/read/29785615/molecular-characterization-of-proton-beam-induced-mutations-in-soybean-using-genotyping-by-sequencing
#16
Woon Ji Kim, Jaihyunk Ryu, Juhyun Im, Sang Hun Kim, Si-Yong Kang, Jeong-Hee Lee, Sung-Hwan Jo, Bo-Keun Ha
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS)...
May 21, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29785397/whole-genome-sequencing-of-greater-amberjack-seriola-dumerili-for-snp-identification-on-aligned-scaffolds-and-genome-structural-variation-analysis-using-parallel-resequencing
#17
Kazuo Araki, Jun-Ya Aokic, Junya Kawase, Kazuhisa Hamada, Akiyuki Ozaki, Hiroshi Fujimoto, Ikki Yamamoto, Hironori Usuki
Greater amberjack ( Seriola dumerili ) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29785135/mutation-analysis-of-brca1-2-mutations-with-special-reference-to-polymorphic-snps-in-indian-breast-cancer-patients
#18
Nidhi D Shah, Parth S Shah, Yash Y Panchal, Kalpesh H Katudia, Nikunj B Khatri, Hari Shankar P Ray, Upti R Bhatiya, Sandip C Shah, Bhavini S Shah, Mandava V Rao
Background: Germline mutations BRCA1 and BRCA2 contribute almost equally in the causation of breast cancer (BC). The type of mutations in the Indian population that cause this condition is largely unknown. Purpose: In this cohort, 79 randomized BC patients were screened for various types of BRCA1 and BRCA2 mutations including frameshift, nonsense, missense, in-frame and splice site types. Materials and methods: The purified extracted DNA of each referral patient was subjected to Sanger gene sequencing using Codon Code Analyzer and Mutation Surveyor and next-generation sequencing (NGS) methods with Ion torrent software, after appropriate care...
2018: Application of Clinical Genetics
https://www.readbyqxmd.com/read/29784899/pathway-based-analysis-of-genome-wide-association-study-of-circadian-phenotypes
#19
Di-di Zhu, Jia-Min Yuan, Rui Zhu, Yao Wang, Zhi-Yong Qian, Jian-Gang Zou
Sleepiness affects normal social life, which attracts more and more attention. Circadian phenotypes contribute to obvious individual differences in susceptibility to sleepiness. We aimed to identify candidate single nucleotide polymorphisms (SNPs) which may cause circadian phenotypes, elucidate the potential mechanisms, and generate corresponding SNP-gene-pathways. A genome-wide association studies (GWAS) dataset of circadian phenotypes was utilized in the study. Then, the Identify Candidate Causal SNPs and Pathways analysis was employed to the GWAS dataset after quality control filters...
November 1, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/29783161/candidate-gene-analysis-in-the-s%C3%A3-o-paulo-epidemiologic-sleep-study-episono-shows-an-association-of-variant-in-pde4d-and-sleepiness
#20
Victoria M Pak, Diego R Mazzotti, Brendan T Keenan, Camila Hirotsu, Philip Gehrman, Lia Bittencourt, Allan I Pack, Sergio Tufik
INTRODUCTION: Sleepiness and cardiovascular disease share common molecular pathways; thus, genetic risk factors for sleepiness may also predict cardiovascular disease risk. This study explored the associations between subjective sleepiness and single-nucleotide polymorphisms (SNPs) in candidate genes within oxidative stress, inflammatory, and neuronal pathways, which may contribute to sleepiness and downstream cardiovascular disease risk: Cytochrome B-245, Alpha Polypeptide (CYBA), Cytochrome B-245, Beta Polypeptide (CYBB), Neutrophil Cytosolic Factor (NCF2), Tumor Necrosis Factor-Alpha (TNFA), and Phosphodiesterase 4D (PDE4D)...
January 12, 2018: Sleep Medicine
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