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Single nucleotide polymorphisms (SNPs)

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https://www.readbyqxmd.com/read/28806841/genetic-polymorphisms-as-predictive-markers-of-response-to-growth-hormone-therapy-in-children-with-growth-hormone-deficiency
#1
Anna Maria Jung, Martin Zenker, Christina Lißewski, Denny Schanze, Stefan Wagenpfeil, Tilman Robert Rohrer
Objective Growth hormone (GH) deficiency (GHD) is commonly treated with recombinant human GH (rhGH). Individual response to rhGH therapy varies widely and there is evidence that variations in growth-related genes, e. g. the GH receptor (GHR) gene, may impact treatment response. We aimed to identify genetic polymorphisms which could serve as predictive markers of response to rhGH therapy. Methods We conducted a genetic analysis of single nucleotide polymorphisms (SNPs) and the GHR exon 3 deletion in 101 paediatric GHD patients receiving rhGH...
August 14, 2017: Klinische Pädiatrie
https://www.readbyqxmd.com/read/28806401/a-gdf15-3-utr-variant-rs1054564-results-in-allele-specific-translational-repression-of-gdf15-by-hsa-mir-1233-3p
#2
Ming-Sheng Teng, Lung-An Hsu, Shu-Hui Juan, Wen-Chi Lin, Ming-Cheng Lee, Cheng-Wen Su, Semon Wu, Yu-Lin Ko
Growth differentiation factor 15 (GDF15) is a strong predictor of cardiovascular events and mortality in individuals with or without cardiovascular diseases. Single nucleotide polymorphisms (SNPs) in microRNA (miRNA) target sites, also known as miRSNPs, are known to enhance or weaken miRNA-mRNA interactions and have been linked to diseases such as cardiovascular disease and cancer. In this study, we aimed to elucidate the functional significance of the miRSNP rs1054564 in regulating GDF15 levels. Two rs1054564-containing binding sites for hsa-miR-873-5p and hsa-miR-1233-3p were identified in the 3' untranslated region (UTR) of the GDF15 transcript using bioinformatics tools...
2017: PloS One
https://www.readbyqxmd.com/read/28805974/effect-of-single-nucleotide-polymorphisms-in-adh1b-adh4-adh1c-oprm1-drd2-bdnf-and-aldh2-genes-on-alcohol-dependence-in-a-caucasian-population
#3
Martha-Spyridoula Katsarou, Konstantinos Karakonstantis, Nikolaos Demertzis, Emmanouil Vourakis, Aspasia Skarpathioti, Aleksandr E Nosyrev, Aristidis Tsatsakis, Theodoris Kalogridis, Nikolaos Drakoulis
Alcohol is a frequently used addictive substance worldwide. Aim of this study is to determine the frequency distribution of SNPs within ADH1B, ADH4, ADH1C, ALDH2, BDNF, OPRM1, and DRD2 genes in a southeastern European Caucasian population from Greece. For this purpose samples of 1276 volunteers were analyzed after deidentification and anonymization. The allele distribution of the examined polymorphisms in the present Greek population cohort was as follows: rs1229984 (ADH1B): GG(wt) = 64.14%, GA = 29.86%, AA = 4...
August 2017: Pharmacology Research & Perspectives
https://www.readbyqxmd.com/read/28804718/cd36-gene-polymorphisms-are-associated-with-intracerebral-hemorrhage-susceptibility-in-a-han-chinese-population
#4
Qiu-Wen Gong, Mao-Fan Liao, Liang Liu, Xiao-Yi Xiong, Qin Zhang, Qi Zhong, Kai Zhou, Yuan-Rui Yang, Zhao-You Meng, Chang-Xiong Gong, Rui Xu, Qing-Wu Yang
The CD36 gene encodes a membrane glycoprotein (type B scavenger receptor, SR-B2) that plays a crucial role in lipid sensing, innate immunity, atherogenesis, and glycolipid metabolism. In this study, we aimed to investigate the association between CD36 gene polymorphisms and intracerebral hemorrhage (ICH) in a Han Chinese population. We performed genotype and allele analyses for eleven single nucleotide polymorphisms (SNPs) of CD36 in a case-controlled study involving 292 ICH patients and 298 control participants...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28804651/pharmacogenetic-biomarkers-to-predict-treatment-response-in-multiple-sclerosis-current-and-future-perspectives
#5
REVIEW
Patricia K Coyle
Disease-modifying therapies (DMTs) have significantly advanced the treatment of relapsing multiple sclerosis (MS), decreasing the frequency of relapses, disability, and magnetic resonance imaging lesion formation. However, patients' responses to and tolerability of DMTs vary considerably, creating an unmet need for biomarkers to identify likely responders and/or those who may have treatment-limiting adverse reactions. Most studies in MS have focused on the identification of pharmacogenetic markers, using either the candidate-gene approach, which requires prior knowledge of the genetic marker and its role in the target disease, or genome-wide association, which examines multiple genetic variants, typically single nucleotide polymorphisms (SNPs)...
2017: Multiple Sclerosis International
https://www.readbyqxmd.com/read/28803404/polymorphisms-in-xrcc1-ercc2-and-ercc3-dna-repair-genes-cyp1a1-xenobiotic-metabolism-gene-and-tobacco-are-associated-with-bladder-cancer-susceptibility-in-tunisian-population
#6
Molka Feki-Tounsi, Rim Khlifi, Ibtihel Louati, Mohamed Fourati, Mohamed-Nabil Mhiri, Amel Hamza-Chaffai, Ahmed Rebai
Other than the established environmental risk factors associated with bladder cancer (BC), little is known about the genetic variations determining the individual susceptibility of this complex disease. This study aimed to investigate the relationship of BC with environmental agents and polymorphisms in XRCC1, ERCC2, and ERCC3 DNA repair genes and CYP1A1, CYP2D6, NAT1, and NAT2 xenobiotic metabolism genes through a hospital-based case-control study in Tunisia. The selection of the single nucleotide polymorphisms (SNPs) (rs25487, rs 13181, rs415407, rs446421, rs1058172, rs4921880, and rs1208) was performed using the dbSNP database...
August 12, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28802359/transmission-analysis-of-tgfb1-gene-polymorphisms-in-non-syndromic-cleft-lip-with-or-without-cleft-palate
#7
Ginila T Raju, Bhaskar V K S Lakkakula, Jyotsna Murthy, Munirajan Arasambattu Kannan, Solomon F D Paul
OBJECTIVES: Transforming growth factor beta1 (TGF-β1) plays a significant role in craniofacial development. Previous linkage studies reported that the TGF-β1-locus at 19q13.1 harbour predisposing genes for non-syndromic oral clefts. In the present study case parents triads were evaluated to find the transmission effects of genetic variants in TGF- β1 towards non-syndromic cleft lip or palate (NSCL/P). METHODS: Using allelic discrimination method148 families (case-parent triads) were assessed for single nucleotide polymorphisms (SNPs) in TGF-β1 gene...
September 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28802078/geographical-features-are-the-predominant-driver-of-molecular-diversification-in-widely-distributed-north-american-whipsnakes
#8
Kyle A O'Connell, Jeffrey W Streicher, Eric N Smith, Matthew K Fujita
Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California, and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28802073/species-delimitation-with-gene-flow-a-methodological-comparison-and-population-genomics-approach-to-elucidate-cryptic-species-boundaries-in-malaysian-torrent-frogs
#9
Kin Onn Chan, Alana M Alexander, Lee L Grismer, Yong-Chao Su, Jesse L Grismer, Evan S H Quah, Rafe M Brown
Accurately delimiting species boundaries is a non-trivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs (mPTP, iBPP, BFD*)...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28801813/detection-of-qtl-for-greasy-fleece-weight-in-sheep-using-a-50%C3%A2-k-single-nucleotide-polymorphism-chip
#10
Fatemeh Ebrahimi, Mohsen Gholizadeh, Ghodrat Rahimi-Mianji, Ayoub Farhadi
Genome-wide association studies (GWAS) have introduced an influential tool in the search for quantitative trait loci (QTL) influencing economically important traits in sheep. To identify QTL associated with greasy fleece weight, a GWAS with 50 K single nucleotide polymorphisms (SNPs) was performed in a Baluchi sheep population. Association with greasy fleece weights was tested using the software Plink. The results of our GWAS provided three novel SNP markers and candidate genes associated with greasy fleece weight...
August 11, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28801681/nrf1-and-zscan10-bind-to-the-promoter-region-of-the-six1-gene-and-their-effects-body-measurements-in-qinchuan-cattle
#11
Da-Wei Wei, Lin-Sheng Gui, Sayed Haidar Abbas Raza, Song Zhang, Rajwali Khan, Li Wang, Hong-Fang Guo, Lin-Sen Zan
The SIX1 homeobox gene belongs to the six homeodomain family and is widely thought to play a principal role in mediating of skeletal muscle development. In the present study, we determined that the bovine SIX1 gene was highly expressed in the longissimus thoracis and physiologically immature individuals. DNA sequencing of 428 individual Qinchuan cattle identified nine single nucleotide polymorphisms (SNPs) in the promoter region of the SIX1 gene. Using a series of 5' deletion promoter plasmid luciferase reporter assays and 5'-rapid amplification of cDNA end analysis (RACE), two of these SNPs were found to be located in the proximal minimal promoter region -216/-28 relative to the transcriptional start site (TSS)...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801593/genetic-variations-of-hvp5cs1-and-their-association-with-drought-tolerance-related-traits-in-barley-hordeum-vulgare-l
#12
Yanshi Xia, Ronghua Li, Guihua Bai, Kadambot H M Siddique, Rajeev K Varshney, Michael Baum, Guijun Yan, Peiguo Guo
Delta-1-pyrroline-5-carboxylate synthase gene1 (P5CS1) is the key gene involved in the biosynthesis of proline and is significantly induced by drought stress. The exploration of genetic variation in HvP5CS1 may facilitate a better understanding of the mechanism of drought adaptation in barley. In the current study, 41 polymorphisms including 16 single nucleotide polymorphisms (SNPs) and 25 insertions/deletions (indels) were detected in HvP5CS1 among 287 barley (Hordeum vulgare L.) accessions collected worldwide, with 13 distinct haplotypes identified in the barley collection...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800731/the-analysis-of-apol1-genetic-variation-and-haplotype-diversity-provided-by-1000-genomes-project
#13
Ting Peng, Li Wang, Guisen Li
BACKGROUND: The APOL1 gene variants has been shown to be associated with an increased risk of multiple kinds of diseases, particularly in African Americans, but not in Caucasians and Asians. In this study, we explored the single nucleotide polymorphism (SNP) and haplotype diversity of APOL1 gene in different races provided by 1000 Genomes project. METHODS: Variants of APOL1 gene in 1000 Genome Project were obtained and SNPs located in the regulatory region or coding region were selected for genetic variation analysis...
August 11, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28800727/a-phased-snp-based-classification-of-sickle-cell-anemia-hbb-haplotypes
#14
Elmutaz M Shaikho, John J Farrell, Abdulrahman Alsultan, Hatem Qutub, Amein K Al-Ali, Maria Stella Figueiredo, David H K Chui, Lindsay A Farrer, George J Murphy, Gustavo Mostoslavsky, Paola Sebastiani, Martin H Steinberg
BACKGROUND: Sickle cell anemia causes severe complications and premature death. Five common β-globin gene cluster haplotypes are each associated with characteristic fetal hemoglobin (HbF) levels. As HbF is the major modulator of disease severity, classifying patients according to haplotype is useful. The first method of haplotype classification used restriction fragment length polymorphisms (RFLPs) to detect single nucleotide polymorphisms (SNPs) in the β-globin gene cluster. This is labor intensive, and error prone...
August 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28800628/genome-wide-analysis-of-sotalol-induced-ikr-inhibition-during-ventricular-repolarization-generepol-study-lack-of-common-variants-with-large-effect-sizes
#15
Joe-Elie Salem, Marine Germain, Jean-Sébastien Hulot, Pascal Voiriot, Bruno Lebourgeois, Jean Waldura, David-Alexandre Tregouet, Beny Charbit, Christian Funck-Brentano
Many drugs used for non-cardiovascular and cardiovascular purposes, such as sotalol, have the side effect of prolonging cardiac repolarization, which can trigger life-threatening cardiac arrhythmias by inhibiting the potassium-channel IKr (KCNH2). On the electrocardiogram (ECG), IKr inhibition induces an increase in QTc and Tpeak-Tend (TpTe) interval and a decrease of T wave maximal amplitude (TAmp). These changes vary markedly between subjects, suggesting the existence of predisposing genetic factors. 990 healthy individuals, prospectively challenged with an oral 80mg sotalol dose, were monitored for changes in ventricular repolarization on ECG between baseline and 3 hours post dosing...
2017: PloS One
https://www.readbyqxmd.com/read/28800603/genetic-variants-specific-to-aging-related-verbal-memory-insights-from-gwass-in-a-population-based-cohort
#16
Thalida E Arpawong, Neil Pendleton, Krisztina Mekli, John J McArdle, Margaret Gatz, Chris Armoskus, James A Knowles, Carol A Prescott
Verbal memory is typically studied using immediate recall (IR) and delayed recall (DR) scores, although DR is dependent on IR capability. Separating these components may be useful for deciphering the genetic variation in age-related memory abilities. This study was conducted to (a) construct individual trajectories in IR and independent aspects of delayed recall, or residualized-DR (rDR), across older adulthood; and (b) identify genetic markers that contribute to four estimated phenotypes: IR and rDR levels and changes after age 60...
2017: PloS One
https://www.readbyqxmd.com/read/28800601/sequence-homology-between-hla-bound-cytomegalovirus-and-human-peptides-a-potential-trigger-for-alloreactivity
#17
Charles E Hall, Vishal N Koparde, Maximilian Jameson-Lee, Abdelrhman G Elnasseh, Allison F Scalora, David J Kobulnicky, Myrna G Serrano, Catherine H Roberts, Gregory A Buck, Michael C Neale, Daniel E Nixon, Amir A Toor
Human cytomegalovirus (hCMV) reactivation may often coincide with the development of graft-versus-host-disease (GVHD) in stem cell transplantation (SCT). Seventy seven SCT donor-recipient pairs (DRP) (HLA matched unrelated donor (MUD), n = 50; matched related donor (MRD), n = 27) underwent whole exome sequencing to identify single nucleotide polymorphisms (SNPs) generating alloreactive peptide libraries for each DRP (9-mer peptide-HLA complexes); Human CMV CROSS (Cross-Reactive Open Source Sequence) database was compiled from NCBI; HLA class I binding affinity for each DRPs HLA was calculated by NetMHCpan 2...
2017: PloS One
https://www.readbyqxmd.com/read/28800512/metabotropic-glutamate-receptors-as-emerging-research-targets-in-bipolar-disorder
#18
REVIEW
Caren J Blacker, Charles P Lewis, Mark A Frye, Marin Veldic
Glutamatergic dysregulation is implicated in the neuropathology of bipolar disorder (BD). There is increasing interest in investigating the role of metabotropic glutamate receptors (mGluRs) in BD and as a target for treatment intervention. Bipolar mGluR studies (published January 1992-April 2016) were identified via PubMed, Embase, Web of Science, and Scopus. Full-text screening, data extraction, and quality appraisal were conducted in duplicate, with strict inclusion and exclusion criteria. The initial literature search for mGluRs in BD, including non-bipolar mood disorders and primary psychotic disorders, identified 1544 articles...
July 31, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28800212/abo-blood-group-phenotype-frequency-estimation-using-molecular-phenotyping-in-rhesus-and-cynomolgus-macaques
#19
S Kanthaswamy, J Ng, R Oldt, L Valdivia, P Houghton, D G Smith
A much larger sample (N = 2369) was used to evaluate a previously reported distribution of the A, AB and B blood group phenotypes in rhesus and cynomolgus macaques from six different regional populations. These samples, acquired from 15 different breeding and research facilities in the US, were analyzed using a real-time quantitative polymerase chain reaction (qPCR) assay that targets single nucleotide polymorphisms (SNPs) responsible for the macaque A, B and AB phenotypes. The frequency distributions of blood group phenotypes of the two species differ significantly from each other, and significant regional differentiation within the geographic ranges of each species was also observed...
August 11, 2017: HLA
https://www.readbyqxmd.com/read/28797660/evaluation-of-genetic-effect-of-nos3-and-g%C3%A3-e-interaction-on-the-variability-of-serum-bilirubin-in-a-han-chinese-population
#20
Yingshui Yao, Zhengmei Fang, Song Yang, Hailong Zhao, Yanchun Chen, Yuelong Jin, Xianghai Zhao, Lijun Zhu, Yuanrui Tian, Chong Shen
Bilirubin was shown to be related to the generation and functional exertion of endothelial nitric oxide synthase (eNOS). However, the genetic effect of NOS3 on bilirubin level was rarely reported. We assessed the associations of single nucleotide polymorphisms (SNPs) of NOS3 (rs4496877, rs1808593, and rs3918186) with bilirubin level in 2077 adults. The results showed that rs1808593 was significantly associated with bilirubin; odds ratios and 95% confidence intervals of dominant models for the elevation of total bilirubin (TBIL), direct bilirubin (DBIL), and indirect bilirubin (IDBIL) were 0...
August 7, 2017: Nitric Oxide: Biology and Chemistry
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