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Single Polymorphism Nucleotide (SNPs)

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https://www.readbyqxmd.com/read/28813039/comparative-assessment-of-ssr-and-snp-markers-for-inferring-the-population-genetic-structure-of-the-common-fungus-armillaria-cepistipes
#1
T Tsykun, C Rellstab, C Dutech, G Sipos, S Prospero
During the last years, simple sequence repeats (SSRs, also known as microsatellites) and single-nucleotide polymorphisms (SNPs) have become the most popular molecular markers for describing neutral genetic variation in populations of a wide range of organisms. However, only a limited number of studies has focused on comparing the performance of these two types of markers for describing the underlying genetic structure of wild populations. Moreover, none of these studies targeted fungi, the group of organisms with one of the most complex reproductive strategies...
August 16, 2017: Heredity
https://www.readbyqxmd.com/read/28812414/adipokine-genes-and-radiographic-hand-osteoarthritis-in-finnish-women-a-cross-sectional-study
#2
S Hämäläinen, S Solovieva, T Vehmas, A Hirvonen, P Leino-Arjas
OBJECTIVES: Available evidence suggests that genetic factors and overweight play major roles in the aetiology of osteoarthritis (OA). We analysed the association of 18 single-nucleotide polymorphisms (SNPs) from nine adipokine and adipokine receptor genes (LEP, LEPR, ADIPOQ, RETN, NAMPT, SERPINA12, ITLN1, RARRES2, and APLN) with radiographic hand OA. METHOD: The study design was cross-sectional. Bilateral hand radiographs of 542 occupationally active Finnish female dentists and teachers aged 45-63 years were examined and classified for the presence of hand OA using reference images...
August 16, 2017: Scandinavian Journal of Rheumatology
https://www.readbyqxmd.com/read/28812116/slco1b1-521t%C3%A2-%C3%A2-c-polymorphism-associated-with-rosuvastatin-induced-myotoxicity-in-chinese-coronary-artery-disease-patients-a-nested-case-control-study
#3
Ju-E Liu, Xiao-Ying Liu, Sheng Chen, Yan Zhang, Li-Yun Cai, Min Yang, Wei-Hua Lai, Bin Ren, Shi-Long Zhong
PURPOSE: This nested case-control study aimed to evaluate the association of candidate genetic variants with statin-induced myotoxicity in Chinese patients with coronary artery disease (CAD). METHODS: One hundred forty-eight Chinese patients experiencing statin-induced myotoxicity were included in our study, and 255 patients without muscular side effects served as controls. Five SNPs in CYP3A5, SLCO1B1, and APOE were genotyped. The effect of genetic variants on statin-induced myotoxicity was assessed...
August 15, 2017: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28811712/association-between-cyp24a1-polymorphisms-and-the-risk-of-colonic-polyps-and-colon-cancer-in-a-chinese-population
#4
Xue-Qi Chen, Jia-Yu Mao, Wen-Bin Li, Jian Li, Hong Yang, Jia-Ming Qian, Jing-Nan Li
AIM: To determine the pathogenesis and potential single nucleotide polymorphisms (SNPs) as screening sites for colonic polyps, colon cancer and ulcerative colitis, and to analyze the possible association between these genetic polymorphisms and the three diseases. METHODS: We evaluated genetic polymorphisms in 144 newly diagnosed colonic polyp patients, 96 colon cancer patients and 44 ulcerative colitis patients. The four SNPs genotyped were rs4809957, rs6068816, rs6091822 and rs8124792...
July 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28811335/the-conserved-and-unique-genetic-architecture-of-kernel-size-and-weight-in-maize-and-rice
#5
Jie Liu, Juan Huang, Huan Guo, Liu Lan, Hongze Wang, Yuancheng Xu, Xiaohong Yang, Wenqiang Li, Hao Tong, Yingjie Xiao, Qingchun Pan, Feng Qiao, Mohammad Sharif Raihan, Haijun Liu, Xuehai Zhang, Ning Yang, Xiaqing Wang, Min Deng, Minliang Jin, Lijun Zhao, Xin Luo, Yang Zhou, Xiang Li, Wei Zhan, Nannan Liu, Hong Wang, Gengshen Chen, Qing Li, Jianbing Yan
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28811306/replication-and-validation-of-genetic-polymorphisms-associated-with-survival-after-allogeneic-blood-or-marrow-transplant
#6
Ezgi Karaesmen, Abbas A Rizvi, Leah Preus, Philip L McCarthy, Marcelo C Pasquini, Kenan Onel, Xiaochun Zhu, Stephen Spellman, Christopher A Haiman, Daniel O Stram, Loreall Pooler, Xin Sheng, Qianqian Zhu, Li Yan, Qian Liu, Qiang Hu, Amy Webb, Guy Brock, Alyssa I Clay-Gilmour, Sebastiano Battaglia, David Tritchler, Song Liu, Theresa Hahn, Lara E Sucheston-Campbell
Multiple candidate gene association studies of non-HLA single nucleotide polymorphisms (SNPs) and outcomes after blood or marrow transplant (BMT) have been conducted. We identified 70 publications reporting 45 SNPs in 36 genes significantly associated with disease-related mortality, progression-free survival, transplant-related mortality and/or overall survival after BMT. Replication and validation of these SNP associations were performed using DISCOVeRY-BMT, a well-powered genome-wide association study consisting of two cohorts, totaling 2,883 BMT recipients with AML, ALL or MDS and their HLA-matched unrelated donors, treated from 2000-2011 and reported to the CIBMTR...
August 15, 2017: Blood
https://www.readbyqxmd.com/read/28810834/multiple-trait-qtl-mapping-and-genomic-prediction-for-wool-traits-in-sheep
#7
Sunduimijid Bolormaa, Andrew A Swan, Daniel J Brown, Sue Hatcher, Nasir Moghaddar, Julius H van der Werf, Michael E Goddard, Hans D Daetwyler
BACKGROUND: The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymorphism (SNP) data. Several key traits determine the value of wool and influence a sheep's susceptibility to fleece rot and fly strike. Our aim was to predict genomic estimated breeding values (GEBV) and to compare three methods of combining information across traits to map polymorphisms that affect these traits...
August 15, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28809852/the-snp-set-based-association-study-identifies-itga1-as-a-susceptibility-gene-of-attention-deficit-hyperactivity-disorder-in-han-chinese
#8
L Liu, L Zhang, H M Li, Z R Wang, X F Xie, J P Mei, J L Jin, J Shi, L Sun, S C Li, Y L Tan, L Yang, J Wang, H M Yang, Q J Qian, Y F Wang
Genome-wide association studies, which detect the association between single-nucleotide polymorphisms (SNPs) and disease susceptibility, have been extensively applied to study attention-deficit/hyperactivity disorder (ADHD), but genome-wide significant associations have not been found yet. Genetic heterogeneity and insufficient genomic coverage may account for the missing heritability. We performed a two-stage association study for ADHD in the Han Chinese population. In the discovery stage, 1033 ADHD patients and 950 healthy controls were genotyped using both the Affymetrix Genome-Wide Human SNP Array 6...
August 15, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28807314/a-candidate-gene-approach-to-study-nematode-resistance-traits-in-naturally-infected-sheep
#9
Hazel Wilkie, Valentina Riggio, Oswald Matika, Louise Nicol, Kathryn A Watt, Rona Sinclair, Alexandra M Sparks, Daniel H Nussey, Josephine M Pemberton, Ross D Houston, John Hopkins
Sheep naturally acquire a degree of resistant immunity to parasitic worm infection through repeated exposure. However, the immune response and clinical outcome vary greatly between animals. Genetic polymorphisms in genes integral to differential T helper cell polarization may contribute to variation in host response and disease outcome. A total of twelve single nucleotide polymorphisms (SNPs) were sequenced in IL23R, RORC2 and TBX21 from genomic DNA of Scottish Blackface lambs. Of the twelve SNPs, six were non-synonymous (missense), four were within the 3' UTRs and two were intronic...
August 30, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28806841/genetic-polymorphisms-as-predictive-markers-of-response-to-growth-hormone-therapy-in-children-with-growth-hormone-deficiency
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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