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https://www.readbyqxmd.com/read/28725161/ep300-single-nucleotide-polymorphism-rs20551-correlates-with-prolonged-overall-survival-in-diffuse-large-b-cell-lymphoma-patients-treated-with-r-chop
#1
Jiao Li, Ning Ding, Xiaogan Wang, Lan Mi, Lingyan Ping, Xuan Jin, Yalu Liu, Zhitao Ying, Yan Xie, Weiping Liu, Yuqin Song, Jun Zhu
BACKGROUND: Rituximab combined with cyclophosphamide, doxorubicin, vincristine and prednisone (CHOP) is used as standard frontline regimen for diffuse large B-cell lymphoma (DLBCL). The landscape of somatic mutations in DLBCL revealed that inactivation of EP300 plays an important role in lymphomagenesis. A common EP300 single nucleotide polymorphism (SNP) rs20551 results in the substitution of valine for isoleucine at codon 997 close to the Bromodomain. However, the association between SNP rs20551 and clinical prognosis in DLBCL patients treated with R-CHOP is unknown...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28724075/a-comprehensive-image-based-phenomic-analysis-reveals-the-complex-genetic-architecture-of-shoot-growth-dynamics-in-rice-oryza-sativa
#2
Malachy T Campbell, Qian Du, Kan Liu, Chris J Brien, Bettina Berger, Chi Zhang, Harkamal Walia
Early vigor is an important trait for many rice ( L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724072/genome-wide-analysis-of-tar-spot-complex-resistance-in-maize-using-genotyping-by-sequencing-snps-and-whole-genome-prediction
#3
Shiliang Cao, Alexander Loladze, Yibing Yuan, Yongsheng Wu, Ao Zhang, Jiafa Chen, Gordon Huestis, Jingsheng Cao, Vijay Chaikam, Michael Olsen, Boddupalli M Prasanna, Felix San Vicente, Xuecai Zhang
Tar spot complex (TSC) is one of the most destructive foliar diseases of maize ( L.) in tropical and subtropical areas of Central and South America, causing significant grain yield losses when weather conditions are conducive. To dissect the genetic architecture of TSC resistance in maize, association mapping, in conjunction with linkage mapping, was conducted on an association-mapping panel and three biparental doubled-haploid (DH) populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs)...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724060/genome-wide-association-mapping-of-crown-rust-resistance-in-oat-elite-germplasm
#4
Kathy Esvelt Klos, Belayneh A Yimer, Ebrahiem M Babiker, Aaron D Beattie, J Michael Bonman, Martin L Carson, James Chong, Stephen A Harrison, Amir M H Ibrahim, Frederic L Kolb, Curt A McCartney, Michael McMullen, Jennifer Mitchell Fetch, Mohsen Mohammadi, J Paul Murphy, Nicholas A Tinker
Oat crown rust, caused by f. sp. , is a major constraint to oat ( L.) production in many parts of the world. In this first comprehensive multienvironment genome-wide association map of oat crown rust, we used 2972 single-nucleotide polymorphisms (SNPs) genotyped on 631 oat lines for association mapping of quantitative trait loci (QTL). Seedling reaction to crown rust in these lines was assessed as infection type (IT) with each of 10 crown rust isolates. Adult plant reaction was assessed in the field in a total of 10 location-years as percentage severity (SV) and as infection reaction (IR) in a 0-to-1 scale...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724058/search-for-dq2-5-and-dq8-alleles-using-a-lower-cost-technique-in-patients-with-type-1-diabetes-and-celiac-disease-in-a-population-of-southern-brazil
#5
Marília D Bastos, Thayne W Kowalski, Márcia Puñales, Balduíno Tschiedel, Luiza M Mariath, Ana Luiza G Pires, Lavínia S Faccini, Themis R Silveira
Objective: To evaluate the frequency of DQ2.5 and DQ8 alleles using the Tag-single-nucleotide polymorphism (Tag-SNP) technique in individuals with type 1 diabetes mellitus (T1DM) and celiac disease (CD) in southern Brazil. Materials and methods: In a prospective design, we performed the search for DQA1*0501 and DQB1*0201 alleles for DQ2.5 and DQB1*0302 for DQ8 through Real-Time Polymerase Chain Reaction (RT-PCR) technique, using TaqMan Genotyping Assays (Applied Biosystems, USA)...
July 13, 2017: Archives of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28723906/genomic-prediction-with-parallel-computing-for-slaughter-traits-in-chinese-simmental-beef-cattle-using-high-density-genotypes
#6
Peng Guo, Bo Zhu, Lingyang Xu, Hong Niu, Zezhao Wang, Long Guan, Yonghu Liang, Hemin Ni, Yong Guo, Yan Chen, Lupei Zhang, Xue Gao, Huijiang Gao, Junya Li
Genomic selection has been widely used for complex quantitative trait in farm animals. Estimations of breeding values for slaughter traits are most important to beef cattle industry, and it is worthwhile to investigate prediction accuracies of genomic selection for these traits. In this study, we assessed genomic predictive abilities for average daily gain weight (ADG), live weight (LW), carcass weight (CW), dressing percentage (DP), lean meat percentage (LMP) and retail meat weight (RMW) using Illumina Bovine 770K SNP Beadchip in Chinese Simmental cattle...
2017: PloS One
https://www.readbyqxmd.com/read/28723867/prediction-of-severe-toxicity-in-adult-patients-under-treatment-with-5-fluorouracil-a-prospective-cohort-study
#7
Carolina Vázquez, María Orlova, Federico Angriman, José N Minatta, Paula Scibona, María A Verzura, Esteban G Jáuregui, Heidy Díaz de Arce, María G Pallotta, Waldo H Belloso
5-Fluorouracil (5-FU) has long been used for the treatment of gastrointestinal tumors harboring interindividual variability in both the pharmacokinetic and the pharmacogenetic profiles, which in turn may lead to life-threatening toxicities. We carried out a prospective cohort study of adult patients initiating treatment with 5-FU between 2013 and 2015. Primary exposures of interest were the methylenetetrahydrofolate reductase single nucleotide polymorphism in exons 4 and 7 and 5'-untranslated region-thymidylate synthase VNTR genotypes, in addition to baseline clinical and demographic variables...
July 18, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/28723497/pharmacogenomic-markers-of-targeted-therapy-toxicity-in-patients-with-metastatic-renal-cell-carcinoma
#8
Guillermo de Velasco, Kathryn P Gray, Lana Hamieh, Yuksel Urun, Hallie A Carol, Andre P Fay, Sabina Signoretti, David J Kwiatkowski, David F McDermott, Matthew Freedman, Mark M Pomerantz, Toni K Choueiri
BACKGROUND: Targeted therapy (TT) in metastatic renal cell carcinoma (mRCC) may be associated with a high rate of toxicity that undermines treatment efficacy and patient quality of life. Polymorphisms in genes involved in the pharmacokinetic pathways of TTs may predict toxicity. OBJECTIVE: To investigate whether selected single-nucleotide polymorphisms (SNPs) in three core genes involved in the metabolism and transport of sunitinib and the mTOR inhibitors everolimus and temsirolimus are associated with adverse events (AEs)...
December 15, 2016: European Urology Focus
https://www.readbyqxmd.com/read/28722347/foxo3-longevity-interactome-on-chromosome-6
#9
Timothy A Donlon, Brian J Morris, Randi Chen, Kamal H Masaki, Richard C Allsopp, D Craig Willcox, Ayako Elliott, Bradley J Willcox
FOXO3 has been implicated in longevity in multiple populations. By DNA sequencing in long-lived individuals, we identified all single nucleotide polymorphisms (SNPs) in FOXO3 and showed 41 were associated with longevity. Thirteen of these had predicted alterations in transcription factor binding sites. Those SNPs appeared to be in physical contact, via RNA polymerase II binding chromatin looping, with sites in the FOXO3 promoter, and likely function together as a cis-regulatory unit. The SNPs exhibited a high degree of LD in the Asian population, in which they define a specific longevity haplotype that is relatively common...
July 19, 2017: Aging Cell
https://www.readbyqxmd.com/read/28719597/pharmacogenomics-study-of-thiazide-diuretics-and-qt-interval-in-multi-ethnic-populations-the-cohorts-for-heart-and-aging-research-in-genomic-epidemiology
#10
A A Seyerle, C M Sitlani, R Noordam, S M Gogarten, J Li, X Li, D S Evans, F Sun, M A Laaksonen, A Isaacs, K Kristiansson, H M Highland, J D Stewart, T B Harris, S Trompet, J C Bis, G M Peloso, J A Brody, L Broer, E L Busch, Q Duan, A M Stilp, C J O'Donnell, P W Macfarlane, J S Floyd, J A Kors, H J Lin, R Li-Gao, T Sofer, R Méndez-Giráldez, S R Cummings, S R Heckbert, A Hofman, I Ford, Y Li, L J Launer, K Porthan, C Newton-Cheh, M D Napier, K F Kerr, A P Reiner, K M Rice, J Roach, B M Buckley, E Z Soliman, R de Mutsert, N Sotoodehnia, A G Uitterlinden, K E North, C R Lee, V Gudnason, T Stürmer, F R Rosendaal, K D Taylor, K L Wiggins, J G Wilson, Y-DI Chen, R C Kaplan, K Wilhelmsen, L A Cupples, V Salomaa, C van Duijn, J W Jukema, Y Liu, D O Mook-Kanamori, L A Lange, R S Vasan, A V Smith, B H Stricker, C C Laurie, J I Rotter, E A Whitsel, B M Psaty, C L Avery
Thiazide diuretics, commonly used antihypertensives, may cause QT interval (QT) prolongation, a risk factor for highly fatal and difficult to predict ventricular arrhythmias. We examined whether common single-nucleotide polymorphisms (SNPs) modified the association between thiazide use and QT or its component parts (QRS interval, JT interval) by performing ancestry-specific, trans-ethnic and cross-phenotype genome-wide analyses of European (66%), African American (15%) and Hispanic (19%) populations (N=78 199), leveraging longitudinal data, incorporating corrected standard errors to account for underestimation of interaction estimate variances and evaluating evidence for pathway enrichment...
July 18, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28718048/joint-effects-of-gwas-snps-in-coagulation-system-confer-risk-to-hypertensive-intracerebral-hemorrhage
#11
Yanyan Cao, Min Tian, Qin Fang, Zheng Wen, Wei Wang, Hu Ding, Dao Wen Wang
Recent genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with coagulation system, including hemostatic factors and hematological phenotypes. However, few articles described the relationships between these SNPs and the risk of hemorrhagic stroke. The aim of our study was to evaluate the roles of these SNPs as risk factors and survival predictors for hemorrhagic stroke. Thirteen SNPs from GWAS in coagulation system were genotyped in a Chinese Han population including 1000 patients with hemorrhagic stroke (intracerebral hemorrhage, ICH = 743; subarachnoid hemorrhage, SAH = 257) and 1044 population-based controls...
July 17, 2017: Neuromolecular Medicine
https://www.readbyqxmd.com/read/28717205/genome-reconstruction-in-cynara-cardunculus-taxa-gains-access-to-chromosome-scale-dna-variation
#12
Alberto Acquadro, Lorenzo Barchi, Ezio Portis, Giulio Mangino, Danila Valentino, Giovanni Mauromicale, Sergio Lanteri
The genome sequence of globe artichoke (Cynara cardunculus L. var. scolymus, 2n = 2x = 34) is now available for use. A survey of C. cardunculus genetic resources is essential for understanding the evolution of the species, carrying out genetic studies and for application of breeding strategies. We report on the resequencing analyses (~35×) of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon. The genomes were reconstructed at a chromosomal scale and structurally/functionally annotated...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717051/detection-of-markers-predictive-of-macrolide-and-fluoroquinolone-resistance-in-mycoplasma-genitalium-from-patients-attending-sexual-health-services-in-england
#13
Rachel Pitt, Helen Fifer, Neil Woodford, Sarah Alexander
OBJECTIVES: Resistance to both macrolides and fluoroquinolones has been reported in Mycoplasma genitalium; however, due to limited diagnostics, studies are often small and confined to specific geographical areas. This study sought to determine the rate of predicted resistance in M. genitalium-positive specimens referred for diagnostic testing. METHODS: Seventy-four M. genitalium-positive specimens, referred to the national reference laboratory (2010-2013) from 19 centres across England, were blinded and anonymised...
July 17, 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/28716390/impact-of-cytokine-genetic-polymorphisms-on-the-risk-of-renal-parenchymal-infection-in-children
#14
Almontaser Hussein, Eman Askar, Ahlam Badawy, Khaled Saad, Asmaa Zahran, Ahmad A Elderwy
BACKGROUND: Acute pyelonephritis is associated with renal scarring in up to 30% of patients. Renal scarring may cause significant long-term morbidity. The pathogenesis of acute pyelonephritis remains unclear, although it involves interaction among uroepithelium, the immune system cells, and the locally produced cytokines. That some UTI-prone children develop acute pyelonephritis, and eventually renal parenchymal scarring, suggests a genetic role. Interleukin-6, interleukin-8, chemokine receptor-1 (CXCR1), and tumor necrosis factor-alpha (TNFα), the key regulators of the host immune responses, are proteins whose secretion is controlled by genes...
July 3, 2017: Journal of Pediatric Urology
https://www.readbyqxmd.com/read/28715844/effects-of-pathogenic-variations-in-the-human-rhodopsin-gene-hrho-on-the-predicted-accessibility-for-a-lead-candidate-ribozyme
#15
Beau R Froebel, Alexandria J Trujillo, Jack M Sullivan
Purpose: The mutation-independent strategy for hammerhead ribozyme (hhRz) or RNA interference (RNAi)-based gene therapeutics to treat autosomal dominant diseases is predicated on the hypothesis that a single therapeutic would equivalently suppress all/most of the diverse mutant mRNAs in patients with the disease phenotype. However, the hypothesis has not been formally tested. We address this through a comprehensive bioinformatics study of how mutations affect target mRNA structure accessibility for a single lead hhRz therapeutic (725GUC↓), designed against human rod rhodopsin mRNA (hRHO), for patients with hRHO mutations that cause autosomal dominant retinitis pigmentosa...
July 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28715704/oxytocin-receptor-gene-polymorphisms-attachment-and-ptsd-results-from-the-national-health-and-resilience-in-veterans-study
#16
Lauren M Sippel, Shizhong Han, Laura E Watkins, Ilan Harpaz-Rotem, Steven M Southwick, John H Krystal, Miranda Olff, Richard Sherva, Lindsay A Farrer, Henry R Kranzler, Joel Gelernter, Robert H Pietrzak
The human oxytocin system is implicated in social behavior and stress recovery. Polymorphisms in the oxytocin receptor gene (OXTR) may interact with attachment style to predict stress-related psychopathology like posttraumatic stress disorder (PTSD). The objective of this study was to examine independent and interactive effects of the OXTR single nucleotide polymorphism (SNP) rs53576, which has been associated with stress reactivity, support-seeking, and PTSD in prior studies, and attachment style on risk for PTSD in a nationally representative sample of 2163 European-American (EA) U...
July 8, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28714006/aldh1l1-variant-rs2276724-and-mrna-expression-predict-post-operative-clinical-outcomes-and-are-associated-with-tp53-expression-in-hbv-related-hepatocellular-carcinoma
#17
Guangzhi Zhu, Xiwen Liao, Chuangye Han, Xiaoguang Liu, Long Yu, Wei Qin, Sicong Lu, Hao Su, Zhiwei Chen, Zhengtao Liu, Yu Liang, Jianlu Huang, Tingdong Yu, Chengkun Yang, Ketuan Huang, Liming Shang, Xinping Ye, Lequn Li, Xue Qin, Kaiyin Xiao, Minhao Peng, Tao Peng
Aldehyde dehydrogenase 1 family member L1 (ALDH1L1) is downregulated in hepatocellular carcinoma (HCC) tumors, and its decreased expression is associated with the poor prognosis of HCC patients. We, therefore, evaluated the effect of single nucleotide polymorphisms (SNPs) of ALDH1L1, and its mRNA expression on the survival of hepatitis B virus (HBV)‑related HCC patients and the association with tumor protein p53 (TP53) expression. ALDH1L1 SNPs in 415 HBV-related HCC patients were genotyped via direct sequencing...
July 14, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28712774/characterization-of-nphs2-gene-polymorphisms-associated-to-steroid-resistance-nephrotic-syndrome-in-indian-children
#18
Bhoomi B Joshi, Kinnari N Mistry, Sishir Gang, Prakash G Koringa, Chaitanya G Joshi
Nephrotic syndrome (NS) is the common glomerular disease in children. These children are treated with steroids, depending upon their behavior. They are either steroid sensitive (SSNS) or steroid resistant (SRNS). NPHS2 gene mutants are linked to the risk of autosomal recessive SRNS and in some cases to SSNS. The present study has been performed to screen single nucleotide polymorphisms (SNPs) of the NPHS2 gene in a group of 90 Indian children suffering with NS (30 SSNS, 30 SRNS and 30 Controls) by PCR method followed by direct exon sequencing...
July 13, 2017: Gene
https://www.readbyqxmd.com/read/28712100/the-role-of-genomic-techniques-in-predicting-response-to-radiation-therapy
#19
REVIEW
Noelle L Williams, Tu Dan, Nicholas G Zaorsky, Shivank Garg, Robert B Den
The understanding of the relationship between genetic variation and an individual patient's response to radiation therapy (RT) has gained significant ground over the past several years. Genetic markers have been identified that could ultimately serve as the foundation for predictive models in clinical practice, and that hold the potential to revolutionize the delivery of precision medicine in oncology. Single nucleotide polymorphisms, single genes, and/or gene signatures could ultimately serve as the basis for patient stratification in prospective clinical trials...
July 15, 2017: Oncology (Williston Park, NY)
https://www.readbyqxmd.com/read/28711986/single-nucleotide-polymorphisms-associated-with-reading-ability-show-connection-to-socio-economic-outcomes
#20
Michelle Luciano, Saskia P Hagenaars, Simon R Cox, William David Hill, Gail Davies, Sarah E Harris, Ian J Deary, David M Evans, Nicholas G Martin, Margaret J Wright, Timothy C Bates
Impairments in reading and in language have negative consequences on life outcomes, but it is not known to what extent genetic effects influence this association. We constructed polygenic scores for difficulties with language and learning to read from genome-wide data in ~6,600 children, adolescents and young adults, and tested their association with health, socioeconomic outcomes and brain structure measures collected in adults (maximal N = 111,749). Polygenic risk of reading difficulties was associated with reduced income, educational attainment, self-rated health and verbal-numerical reasoning (p < 0...
July 15, 2017: Behavior Genetics
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