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https://www.readbyqxmd.com/read/28453813/identification-and-allelic-dissection-uncover-roles-of-lncrnas-in-secondary-growth-of-populus-tomentosa
#1
Daling Zhou, Qingzhang Du, Jinhui Chen, Qingshi Wang, Deqiang Zhang
Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation...
April 26, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28453702/a-phase-2-randomized-double-blind-placebo-%C3%A2-controlled-study-of-chemo-immunotherapy-combination-using-motolimod-with-pegylated-liposomal-doxorubicin-in-recurrent-or-persistent-ovarian-cancer-a-gynecologic-oncology-group-partners-study
#2
B J Monk, M F Brady, C Aghajanian, H A Lankes, T Rizack, J Leach, J M Fowler, R Higgins, P Hanjani, M Morgan, R Edwards, W Bradley, T Kolevska, P Foukas, E M Swisher, K S Anderson, R Gottardo, J K Bryan, M Newkirk, K L Manjarrez, R S Mannel, R M Hershberg, G Coukos
Background: A phase 2, randomized, placebo-controlled trial was conducted in women with recurrent epithelial ovarian carcinoma to evaluate the efficacy and safety of motolimod-a Toll-like receptor 8 (TLR8) agonist that stimulates robust innate immune responses-combined with pegylated liposomal doxorubicin (PLD), a chemotherapeutic that induces immunogenic cell death. Patients and methods: Women with ovarian, fallopian tube, or primary peritoneal carcinoma were randomized 1 : 1 to receive PLD in combination with blinded motolimod or placebo...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453699/microrna-related-genetic-variants-in-iron-regulatory-genes-dietary-iron-intake-micrornas-and-lung-cancer-risk
#3
L Zhang, Y Ye, H Tu, M A Hildebrandt, L Zhao, J V Heymach, J A Roth, X Wu
Background: Genetic variations in MicroRNA (miRNA) binding sites may alter structural accessibility of miRNA binding sites to modulate risk of cancer. This large-scale integrative multistage study was aimed to evaluate the interplay of genetic variations in miRNA binding sites of iron regulatory pathway, dietary iron intake and lung cancer (LC) risk. Patients and methods: The interplay of genetic variant, dietary iron intake and LC risk was assessed in large-scale case-control study...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453695/genetic-variants-of-dna-repair-related-genes-predict-efficacy-of-tas-102-in-patients-with-refractory-metastatic-colorectal-cancer
#4
M Suenaga, M Schirripa, S Cao, W Zhang, D Yang, S Murgioni, D Rossini, F Marmorino, A Mennitto, Y Ning, S Okazaki, M D Berger, Y Miyamoto, R Gopez, A Barzi, T Yamaguchi, F Loupakis, H-J Lenz
Background: Tri-phosphorylated trifluridine (FTD) incorporation into DNA is TAS-102's main anti-tumor action. We tested whether genetic polymorphisms in homologous recombination (HR) and cell cycle checkpoint pathway for DNA repair is associated with outcomes in refractory metastatic colorectal cancer (mCRC) patients treated with TAS-102. Patients and methods: We analyzed genomic DNA extracted from 233 samples of three cohorts: an evaluation cohort of 52 patients receiving TAS-102, a validation cohort of 129 patients receiving TAS-102 and a control cohort of 52 patients receiving regorafenib...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453396/pharmacogenetic-analysis-of-hepatitis-c-virus-related-mixed-cryoglobulinemia
#5
Jessica Cusato, Lucio Boglione, Amedeo De Nicolò, Chiara Simona Cardellino, Chiara Carcieri, Giuseppe Cariti, Giovanni Di Perri, Antonio D'Avolio
AIM: Mixed cryoglobulinemia (MC) is an extra hepatic hepatitis C virus related problem and different studies suggested genetics' role in predicting this complication. We evaluated the influence of SNPs in IL-28B, SLC29A1, SLC28A2, NT5C2, HNF4 and ABCB1 genes in MC prediction. PATIENTS & METHODS: SNPs were evaluated through real-time PCR. RESULTS:  ABCB1 (gene encoding P-glycoprotein) 3435C>T SNP was associated with MC presence (p = 0.034): related to T allele carriers (CC vs CT/TT), we reached a p-value of 0...
April 28, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28453395/association-of-vitamin-d-pathway-snps-and-clinical-response-to-interferon-in-a-cohort-of-hbeag-negative-patients
#6
Jessica Cusato, Lucio Boglione, Amedeo De Nicolò, Rosaria Imbornone, Chiara Simona Cardellino, Valeria Ghisetti, Chiara Carcieri, Giuseppe Cariti, Giovanni Di Perri, Antonio D'Avolio
AIM: Vitamin D modulates biological processes; an influence of vitamin D levels and genetic variants was identified concerning hepatitis B virus infection. We evaluated the role of some SNPs of vitamin D pathway genes in some clinical features of hepatitis B affected patients treated with pegylated interferon. METHODS: We investigated SNPs in IL-28B, CYP27B1, CYP27A1, CYP24A1, VDBP and VDR genes, through real-time PCR. RESULTS:  VDRApaI SNP was associated to viral load and HBsAg presence at different timings...
April 28, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28446629/vitamin-d-receptor-and-megalin-gene-polymorphisms-are-associated-with-longitudinal-cognitive-change-among-african-american-urban-adults
#7
May A Beydoun, Salman M Tajuddin, Greg A Dore, Jose-Atilio Canas, Hind A Beydoun, Michele K Evans, Alan B Zonderman
Background: The link between longitudinal cognitive change and polymorphisms in the vitamin D receptor (VDR) and MEGALIN [or LDL receptor-related protein 2 (LRP2)] genes remains unclear, particularly among African-American (AA) adults.Objectives: We aimed to evaluate associations of single nucleotide polymorphisms (SNPs) for VDR [rs11568820 (Cdx-2:T/C), rs1544410 (BsmI:G/A), rs7975232 (ApaI:A/C), rs731236 (TaqI:G/A)] and LRP2 [rs3755166:G/A,rs2075252:C/T, rs2228171:C/T] genes with longitudinal cognitive performance change in various domains of cognition...
April 26, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28446577/population-dynamics-of-staphylococcus-aureus-in-cystic-fibrosis-patients-to-determine-transmission-events-utilizing-wgs
#8
Andrea Ankrum, Barry G Hall
Strict infection control practices have been implemented for healthcare visits by Cystic Fibrosis patients in an attempt to prevent transmission of important pathogens. This study used whole genome sequencing (WGS) to determine strain relatedness and assess population dynamics of Staphylococcus aureus isolates from a cohort of CF patients as assessed by strain relatedness. 311 S. aureus isolates were collected from respiratory cultures of 115 CF patients during a 22 month study period. Whole genome sequencing was performed and using SNP analysis, phylogenetic trees were assembled to determine relatedness between isolates...
April 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28445979/the-impacts-of-single-nucleotide-polymorphisms-in-genes-of-cell-cycle-and-nf-kb-pathways-on-the-efficacy-and-acute-toxicities-of-radiotherapy-in-patients-with-nasopharyngeal-carcinoma
#9
Chengxian Guo, Yuling Huang, Jingjing Yu, Lijuan Liu, Xiaochang Gong, Min Huang, Chunling Jiang, Yulu Liao, Lihua Huang, Guoping Yang, Jingao Li
Radiotherapy is one of the primary choices for the treatment of nasopharyngeal carcinoma (NPC) and may result in severe radiotoxicities on normal tissues. Single nucleotide polymorphisms (SNPs) in genes of cell cycle and NF-κB pathways have been linked with the prognoses of various cancers. The aim of this study was to explore whether SNPs of genes involved in cell cycle and NF-κB pathways are associated with responses to radiotherapy in NPC patients. We selected 3 SNPs in cell cycle pathway and 5 SNPs in NF-κB pathway and genotyped them in 154 NPC patients treated with radiotherapy...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445614/two-common-human-cldn5-alleles-encode-different-open-reading-frames-but-produce-one-protein-isoform
#10
Ronald M Cornely, Barbara Schlingmann, Whitney S Shepherd, Joshua D Chandler, David C Neujahr, Michael Koval
Claudins provide tight junction barrier selectivity. The human CLDN5 gene contains a high-frequency single-nucleotide polymorphism (rs885985), where the G allele codes for glutamine (Q) and the A allele codes for an amber stop codon. Thus, these different CLDN5 alleles define nested open reading frames (ORFs) encoding claudin-5 proteins that are 303 or 218 amino acids in length. Interestingly, human claudin-16 and claudin-23 also have long ORFs. The long form of claudin-5 contrasts with the majority of claudin-5 proteins in the National Center for Biotechnology Information protein database, which are less than 220 amino acids in length...
April 26, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28445130/single-nucleotide-polymorphisms-in-mlh1-predict-poor-prognosis-of-hepatocellular-carcinoma-in-a-chinese-population
#11
Xiaonian Zhu, Wei Liu, Xiaoqiang Qiu, Zhigang Wang, Chao Tan, Chunhua Bei, Linyuan Qin, Yuan Ren, Shengkui Tan
Hepatocellular carcinoma (HCC) is a malignant cancer causing deleterious health effect worldwide, especially in China. So far clinical cure rate and long-term survival rate of HCC remains low. Most HCC patients after cancer resection have recurrence or metastasis within 5 years. This study aims to explore the genetic association of mutL homolog 1 (MLH1) polymorphisms with HCC risk and prognosis. Four candidate MLH1 polymorphisms, rs1800734, rs10849, rs3774343 and rs1540354 were studied from a hospital-based case-control study including 1,036 cases (HCC patients) and 1,036 controls (non-HCC patients) in Guangxi, China...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444748/identification-of-coagulation-gene-3-utr-variants-that-are-potentially-regulated-by-micrornas
#12
Carla Y Vossen, Astrid van Hylckama Vlieg, Raúl Teruel-Montoya, Salam Salloum-Asfar, Hugoline de Haan, Javier Corral, Pieter Reitsma, Bobby P C Koeleman, Constantino Martínez
MicroRNAs have been recognized as critical regulators of gene expression and might affect the risk of venous thrombosis. We aimed to identify 3' untranslated region (UTR) variants in coagulation genes that influence coagulation factor levels and venous thrombosis risk. The 3'UTR of coagulation genes were sequenced in subjects with extremely high or low plasma levels of these factors in two case-control studies. In total, 28 variants were identified. Five single nucleotide polymorphisms (SNPs) were predominantly present in one extreme level group (F2 rs1799963, F8 rs1050705 and F11 rs4253429, rs4253430 and rs1062547)...
April 26, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28443323/prevalence-of-ctr1-and-ercc1-polymorphisms-and-response-of-biliary-tract-cancer-to-gemcitabine-platinum-chemotherapy
#13
Skolchart Pongmaneratanakul, Suebpong Tanasanvimon, Thitima Pengsuparp, Nutthada Areepium
Purpose: Biliary tract cancer (BTC)is an aggressive disease with a poor prognosis. Most patients are diagnosed at an advanced stage for which curative surgery is not possible and gemcitabine-platinum chemotherapy is the treatment of choice for advanced cases. Several studies had focused on biomarkers to predict response from platinum drugs in lung cancer, but information is limited for BTC. In this study, two single nucleotide polymorphisms (SNPs) in the copper transporter (CTR1) and excision repair cross-complementary group 1 (ERCC1) genes were investigated as predictive biomarkers of objective response to gemcitabine-platinum...
March 1, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/28442232/a-genetic-risk-score-predicts-cardiovascular-events-in-patients-with-stable-coronary-artery-disease
#14
Morten Krogh Christiansen, Mette Nyegaard, Sanne Bøjet Larsen, Erik Lerkevang Grove, Morten Würtz, Søs Neergaard-Petersen, Anne-Mette Hvas, Henrik Kjærulf Jensen, Steen Dalby Kristensen
BACKGROUND: Genetic risk scores (GRSs) may predict cardiovascular risk in community-based populations. However, studies investigating the association with recurrent cardiovascular events in patients with established coronary artery disease (CAD) are conflicting. METHODS: We genotyped 879 patients with high-risk stable CAD and created a GRS based on 45 single nucleotide polymorphisms previously reported to be associated with CAD in genome-wide association studies...
April 19, 2017: International Journal of Cardiology
https://www.readbyqxmd.com/read/28441070/the-thr300ala-variant-of-atg16l1-is-associated-with-decreased-risk-of-brain-metastasis-in-patients-with-non-small-cell-lung-cancer
#15
Qian-Xia Li, Xiao Zhou, Ting-Ting Huang, Yang Tang, Bo Liu, Ping Peng, Li Sun, Yi-Hua Wang, Xiang-Lin Yuan
Non-small cell lung cancer (NSCLC) often metastasizes to the brain, but identifying which patients will develop brain metastases (BM) is difficult. Macroautophagy/autophagy is critical for cancer initiation and progression. We hypothesized that genetic variants of autophagy-related genes may affect brain metastases (BM) in NSCLC patients. We genotyped 16 single nucleotide polymorphisms (SNPs) in 7 autophagy-related (ATG) genes (ATG3, ATG5, ATG7, ATG10, ATG12, ATG16L1, and MAP1LC3/LC3) by using DNA from blood samples of 323 NSCLC patients...
April 25, 2017: Autophagy
https://www.readbyqxmd.com/read/28440410/a-novel-notch3-mutation-identified-in-patients-with-oral-cancer-by-whole-exome-sequencing
#16
Yanjun Yi, Zhuowei Tian, Houyu Ju, Guoxin Ren, Jingzhou Hu
Oral cancer is a serious disease caused by environmental factors and/or susceptible genes. In the present study, in order to identify useful genetic biomarkers for cancer prediction and prevention, and for personalized treatment, we detected somatic mutations in 5 pairs of oral cancer tissues and blood samples using whole exome sequencing (WES). Finally, we confirmed a novel nonsense single-nucleotide polymorphism (SNP; chr19:15288426A>C) in the NOTCH3 gene with sanger sequencing, which resulted in a N1438T mutation in the protein sequence...
April 25, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28439286/snp-discovery-and-genetic-variation-of-candidate-genes-relevant-to-heat-tolerance-and-agronomic-traits-in-natural-populations-of-sand-rice-agriophyllum-squarrosum
#17
Pengshan Zhao, Jiwei Zhang, Chaoju Qian, Qin Zhou, Xin Zhao, Guoxiong Chen, Xiao-Fei Ma
The extreme stress tolerance and high nutritional value of sand rice (Agriophyllum squarrosum) make it attractive for use as an alternative crop in response to concerns about ongoing climate change and future food security. However, a lack of genetic information hinders understanding of the mechanisms underpinning the morphological and physiological adaptations of sand rice. In the present study, we sequenced and analyzed the transcriptomes of two individuals representing semi-arid [Naiman (NM)] and arid [Shapotou (SPT)] sand rice genotypes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439101/largest-gwas-of-ptsd-n-20%C3%A2-070-yields-genetic-overlap-with-schizophrenia-and-sex-differences-in-heritability
#18
L E Duncan, A Ratanatharathorn, A E Aiello, L M Almli, A B Amstadter, A E Ashley-Koch, D G Baker, J C Beckham, L J Bierut, J Bisson, B Bradley, C-Y Chen, S Dalvie, L A Farrer, S Galea, M E Garrett, J E Gelernter, G Guffanti, M A Hauser, E O Johnson, R C Kessler, N A Kimbrel, A King, N Koen, H R Kranzler, M W Logue, A X Maihofer, A R Martin, M W Miller, R A Morey, N R Nugent, J P Rice, S Ripke, A L Roberts, N L Saccone, J W Smoller, D J Stein, M B Stein, J A Sumner, M Uddin, R J Ursano, D E Wildman, R Yehuda, H Zhao, M J Daly, I Liberzon, K J Ressler, C M Nievergelt, K C Koenen
The Psychiatric Genomics Consortium-Posttraumatic Stress Disorder group (PGC-PTSD) combined genome-wide case-control molecular genetic data across 11 multiethnic studies to quantify PTSD heritability, to examine potential shared genetic risk with schizophrenia, bipolar disorder, and major depressive disorder and to identify risk loci for PTSD. Examining 20 730 individuals, we report a molecular genetics-based heritability estimate (h(2)SNP) for European-American females of 29% that is similar to h(2)SNP for schizophrenia and is substantially higher than h(2)SNP in European-American males (estimate not distinguishable from zero)...
April 25, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28438693/effects-of-four-novel-genetic-polymorphisms-on-clopidogrel-efficacy-in-chinese-acute-coronary-syndromes-patients
#19
Fei-Yan Xiao, Min Liu, Bi-Lian Chen, Shan Cao, Lan Fan, Zhao-Qian Liu, Hong-Hao Zhou, Wei Zhang, Gan Zhou
Dual antiplatelet therapy is the gold standard for the clinical treatment of coronary artery disease, especially for acute coronary syndromes patients. However, a substantial number of patients do not respond to clopidogrel despite a standardized dosage regimen, and this is directly associated with poor prognosis. Genetic polymorphisms may be one of the most important factors that contribute to this phenomenon. In this study, we aimed to detect new single nucleotide polymorphisms that can influence the efficacy of clopidogrel in 851 acute coronary syndromes (ACS) patients...
April 21, 2017: Gene
https://www.readbyqxmd.com/read/28437488/the-novel-carboxylesterase-1-variant-c-662a-g-may-decrease-the-bioactivation-of-oseltamivir-in-humans
#20
Jaeseong Oh, SeungHwan Lee, Howard Lee, Joo-Youn Cho, Seo Hyun Yoon, In-Jin Jang, Kyung-Sang Yu, Kyoung Soo Lim
BACKGROUND: Human carboxylesterase 1 (CES1) is a serine esterase that hydrolyses various exogenous and endogenous compounds including oseltamivir, a prodrug used to treat influenza. A novel CES1 c.662A>G single nucleotide polymorphism (SNP) was predicted to decrease CES1 enzymatic activity in an in silico analysis. This study evaluated the effect of the c.662A>G SNP on the pharmacokinetics (PK) of oseltamivir in humans. METHODS: A single oral dose of oseltamivir at 75 mg was administered to 20 healthy subjects, 8 heterozygous c...
2017: PloS One
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