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Single Polymorphism Nucleotide (SNPs)

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https://www.readbyqxmd.com/read/28340513/mendelian-randomisation-implicates-hyperlipidaemia-as-a-risk-factor-for-colorectal-cancer
#1
Henry Rodriguez-Broadbent, Philip J Law, Amit Sud, Kimmo Palin, Sari Tuupanen, Alexandra Gylfe, Ulrika A Hänninen, Tatiana Cajuso, Tomas Tanskanen, Johanna Kondelin, Eevi Kaasinen, Antti-Pekka Sarin, Samuli Ripatti, Johan G Eriksson, Harri Rissanen, Paul Knekt, Eero Pukkala, Pekka Jousilahti, Veikko Salomaa, Aarno Palotie, Laura Renkonen-Sinisalo, Anna Lepistö, Jan Böhm, Jukka-Pekka Mecklin, Nada A Al-Tassan, Claire Palles, Lynn Martin, Ella Barclay, Susan M Farrington, Maria N Timofeeva, Brian F Meyer, Salma M Wakil, Harry Campbell, Christopher G Smith, Shelley Idziaszczyk, Timothy S Maughan, Richard Kaplan, Rachel Kerr, David Kerr, Michael N Passarelli, Jane C Figueiredo, Daniel D Buchanan, Aung K Win, John L Hopper, Mark A Jenkins, Noralane M Lindor, Polly A Newcomb, Steven Gallinger, David Conti, Fred Schumacher, Graham Casey, Lauri A Aaltonen, Jeremy P Cheadle, Ian P Tomlinson, Malcolm G Dunlop, Richard S Houlston
While elevated blood cholesterol has been associated with an increased risk of colorectal cancer (CRC) in observational studies, causality is uncertain. Here we apply a Mendelian randomisation (MR) analysis to examine the potential causal relationship between lipid traits and CRC risk. We used single nucleotide polymorphisms (SNPs) associated with blood levels of total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) as instrumental variables (IV). We calculated MR estimates for each risk factor with CRC using SNP-CRC associations from 9,254 cases and 18,386 controls...
March 24, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28340271/snp-detection-using-rna-sequences-of-candidate-genes-associated-with-puberty-in-cattle
#2
M M Dias, A Cánovas, C Mantilla-Rojas, D G Riley, P Luna-Nevarez, S J Coleman, S E Speidel, R M Enns, A Islas-Trejo, J F Medrano, S S Moore, M R S Fortes, L T Nguyen, B Venus, I S D P Diaz, F R P Souza, L F S Fonseca, F Baldi, L G Albuquerque, M G Thomas, H N Oliveira
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340265/association-of-runx2-and-tnfsf11-genes-with-production-traits-in-a-paternal-broiler-line
#3
N V Grupioni, N B Stafuzza, A B Carvajal, A M G Ibelli, J O Peixoto, M C Ledur, D P Munari
Intense selection for production traits has improved the genetic gain of important economic traits. However, selection for performance and carcass traits has led to the onset of locomotors problems and decreasing bone strength in broilers. Thus, genes associated with bone integrity traits have become candidates for genetic studies in order to reduce the impact of bone disorders in broilers. This study investigated the association of the RUNX2 and TNFSF11 genes with 79 traits related to performance, carcass composition, organs, and bone integrity in a paternal broiler line...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28339850/allelic-variation-in-tlr4-is-linked-to-resistance-to-salmonella-enteritidis-infection-in-chickens
#4
Peng Li, Huihua Wang, Xingwang Zhao, Zhongyong Gou, Ranran Liu, Yongmei Song, Qinghe Li, Maiqing Zheng, Huanxian Cui, Nadia Everaert, Guiping Zhao, Jie Wen
Salmonella Enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Polymorphisms of the TLR4 gene may affect recognition by Toll-like receptor 4 (TLR4) of bacterial lipopolysaccharide (LPS), leading to differences in host resistance to pathogenic infections. The present study has investigated polymorphic loci of chicken TLR4 (ChTLR4) in ten chicken breeds, electrostatic potentials of mutant structures of TLR4, and a linkage analysis between allelic variation and survival ratio to infection with SE in specific-pathogen-free (SPF) White Leghorns...
March 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#5
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28339009/identification-of-egflam-spatc1l-and-rnase13-as-novel-susceptibility-loci-for-aortic-aneurysm-in-japanese-individuals-by-exome-wide-association-studies
#6
Yoshiji Yamada, Jun Sakuma, Ichiro Takeuchi, Yoshiki Yasukochi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Masaaki Muramatsu, Motoji Sawabe, Yoshinori Fujiwara, Yu Taniguchi, Shuichi Obuchi, Hisashi Kawai, Shoji Shinkai, Seijiro Mori, Tomio Arai, Masashi Tanaka
We performed an exome-wide association study (EWAS) to identify genetic variants - in particular, low‑frequency or rare variants with a moderate to large effect size - that confer susceptibility to aortic aneurysm with 8,782 Japanese subjects (456 patients with aortic aneurysm, 8,326 control individuals) and with the use of Illumina HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays. The correlation of allele frequencies for 41,432 single nucleotide polymorphisms (SNPs) that passed quality control to aortic aneurysm was examined with Fisher's exact test...
March 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338794/genome-wide-association-study-unravels-the-genetic-control-of-the-apple-volatilome-and-its-interplay-with-fruit-texture
#7
Brian Farneti, Mario Di Guardo, Iuliia Khomenko, Luca Cappellin, Franco Biasioli, Riccardo Velasco, Fabrizio Costa
Fruit quality represents a fundamental factor guiding consumers' preferences. Among apple quality traits, volatile organic compounds and texture features play a major role. Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-ToF-MS), coupled with an artificial chewing device, was used to profile the entire apple volatilome of 162 apple accessions, while the fruit texture was dissected with a TAXT-AED texture analyzer. The array of volatile compounds was classed into seven major groups and used in a genome-wide association analysis carried out with 9142 single nucleotide polymorphisms (SNPs)...
February 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338112/pnpla3-and-rnf7-gene-variants-are-associated-with-the-risk-of-developing-liver-fibrosis-and-cirrhosis-in-an-eastern-european-population
#8
Juozas Kupcinskas, Irena Valantiene, Greta Varkalaitė, Ruta Steponaitiene, Jurgita Skieceviciene, Jolanta Sumskiene, Vitalija Petrenkiene, Jurate Kondrackiene, Gediminas Kiudelis, Frank Lammert, Limas Kupcinskas
BACKGROUND AND AIMS: Genome-wide association studies have revealed an association between the risk of developing liver fibrosis or cirrhosis and the single nucleotide polymorphisms (SNPs) of the PNPLA3, RNF7, MERTK and PCSK7 genes. We aimed to validate these results in an Eastern European population. METHODS: We evaluated the associations between the PNPLA3 (rs738409), RNF7 (rs16851720), MERTK (rs4374383) and PCSK7 (rs236918) variants and liver fibrosis and cirrhosis in a series of consecutive patients recruited at the Department of Gastroenterology, Lithuanian University of Health Sciences Hospital, during the period 2012-2015...
March 2017: Journal of Gastrointestinal and Liver Diseases: JGLD
https://www.readbyqxmd.com/read/28337273/t-box-family-of-transcription-factor-tbx5-insights-in-development-and-disease
#9
Ting Zhu, Longwei Qiao, Qian Wang, Rui Mi, Jinnan Chen, Yaojuan Lu, Junxia Gu, Qiping Zheng
The T-box gene family refers to a group of transcription factors that share a highly conserved, sequence-specific DNA-binding domain (T-box) containing around 180-amino acids. According to HUGO gene nomenclature committee (HGNC), there are 18 T-box family members. These T-box genes have been implicated essential roles during embryogenesis and cardiac development, given their specific expression pattern in developing mammalian heart for several T-box genes, including TBX5. TBX5 is consisted of three transcriptional variants which cover 9 exons and encode two distinct isoforms that differ in N-terminus...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28336767/correlations-between-ace-single-nucleotide-polymorphisms-and-prognosis-of-patients-with-septic-shock
#10
Xin-Man Dou, Yu-Min Li, Hui-Juan Cheng, Ling Meng, Lin-Lin Zhou, Yi-Hong Ke, Li-Ping Liu
The aim of this study is to investigate association between septic shock (SS) and ACE single nucleotide polymorphisms (SNPs). From October 2009 to December 2015, 238 SS patients and 242 healthy individuals were selected for our study. ACE activity was detected, ACE rs4291 and rs4646994 polymorphisms were detected using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The Kaplan-Meier survival curve was employed to evaluate association between ACE SNPs and patient survival, and univariate and multivariate analyses to estimate risk factors for SS...
March 23, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28336495/genetic-variation-and-epigenetic-modification-of-the-prodynorphin-gene-in-peripheral-blood-cells-in-alcoholism
#11
Claudio D'Addario, Klementy Shchetynsky, Mariangela Pucci, Carlo Cifani, Agneta Gunnar, Vladana Vukojević, Leonid Padyukov, Lars Terenius
Dynorphins are critically involved in the development, maintenance and relapse of alcoholism. Alcohol-induced changes in the prodynorphin gene expression may be influenced by both gene polymorphisms and epigenetic modifications. The present study of human alcoholics aims to evaluate DNA methylation patterns in the prodynorphin gene (PDYN) promoter and to identify single nucleotide polymorphisms (SNPs) associated with alcohol dependence and with altered DNA methylation. Genomic DNA was isolated from peripheral blood cells of alcoholics and healthy controls, and DNA methylation was studied in the PDYN promoter by bisulfite pyrosequencing...
March 20, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28335481/genetic-variants-contributing-to-colistin-cytotoxicity-identification-of-tgif1-and-hoxd10-using-a-population-genomics-approach
#12
Michael T Eadon, Ronald J Hause, Amy L Stark, Ying-Hua Cheng, Heather E Wheeler, Kimberly S Burgess, Eric A Benson, Patrick N Cunningham, Robert L Bacallao, Pierre C Dagher, Todd C Skaar, M Eileen Dolan
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines...
March 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335376/genetic-polymorphisms-contribute-to-the-individual-variations-of-imatinib-mesylate-plasma-levels-and-adverse-reactions-in-chinese-gist-patients
#13
Jing Liu, Zhiyu Chen, Hanmei Chen, Yingyong Hou, Weiqi Lu, Junyi He, Hanxing Tong, Yuhong Zhou, Weimin Cai
Imatinib mesylate (IM) has dramatically improved the outcomes of gastrointestinal stromal tumor (GIST) patients. However, the clinical responses of IM may considerably vary among single individuals. This study aimed to investigate the influences of genetic polymorphisms of drug-metabolizing enzyme (CYP3A4), transporters (ABCB1, ABCG2), and nuclear receptor (Pregnane X Receptor (PXR, encoded by NR1I2)) on IM plasma levels and related adverse reactions in Chinese GIST patients. A total of 68 Chinese GIST patients who have received IM 300-600 mg/day were genotyped for six single nucleotide polymorphisms (SNPs) (CYP3A4 rs2242480; ABCB1 rs1045642; ABCG2 rs2231137; NRI12 rs3814055, rs6785049, rs2276706), and the steady-state IM trough plasma concentrations were measured by a validated HPLC method...
March 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334950/downstream-targets-of-gwas-detected-genes-for-breast-lung-and-prostate-and-colon-cancer-converge-to-g1-s-transition-pathway
#14
Olga Y Gorlova, Eugene I Demidenko, Christopher I Amos, Ivan P Gorlov
Genome-wide association studies (GWASs) identified over 500 single nucleotide polymorphisms (SNPs) influencing cancer risk. It is logical to expect the cancer-associated genes to cluster in pathways directly involved in carcinogenesis, e.g. cell cycle. Nevertheless, analyses of the GWAS-detected cancer risk genes usually show no or weak enrichment by known cancer genes.We hypothesized that GWAS-detected cancer risk-associated genes function as upstream regulators of the genes directly involved in carcinogenesis...
March 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334342/tagging-snp-set-selection-with-maximum-information-based-on-linkage-disequilibrium-structure-in-genome-wide-association-studies
#15
Shudong Wang, Sicheng He, Fayou Yuan, Xinjie Zhu
Motivation: Effective tagging single-nucleotide polymorphism (SNP)-set selection is crucial to SNP-set analysis in genome-wide association studies (GWAS). Most of the existing tagging SNP-set selection methods cannot make full use of the information hidden in common or rare variants associated diseases. It is noticed that some SNPs have overlapping genetic information owing to linkage disequilibrium (LD) structure between SNPs. Therefore, when testing the association between SNPs and disease susceptibility, it is sufficient to elect the representative SNPs (called tag SNP-set or tagSNP-set) with maximum information...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334241/rmats-dvr-rmats-discovery-of-differential-variants-in-rna
#16
Jinkai Wang, Yang Pan, Shihao Shen, Lan Lin, Yi Xing
Motivation: RNA sequences of a gene can have single nucleotide variants (SNVs) due to single nucleotide polymorphisms (SNPs) in the genome, or RNA editing events within the RNA. By comparing RNA-seq data of a given cell type before and after a specific perturbation, we can detect and quantify SNVs in the RNA and discover SNVs with altered frequencies between distinct cellular states. Such differential variants in RNA (DVRs) may reflect allele-specific changes in gene expression or RNA processing, as well as changes in RNA editing in response to cellular perturbations or stimuli...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334237/dna-compass-a-secure-client-side-site-for-navigating-personal-genetic-information
#17
Charles Curnin, Assaf Gordon, Yaniv Erlich
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data - an impediment for the general public. Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334234/breast-cancer-risk-associated-variants-at-6q25-1-influence-risk-of-hepatocellular-carcinoma-in-a-chinese-population
#18
Jiaoyuan Li, Ying Wang, Ying Zhu, Yajie Gong, Yang Yang, Jianbo Tian, Yi Zhang, Danyi Zou, Xiating Peng, Juntao Ke, Jing Gong, Rong Zhong, Jiang Chang
The gender disparity observed in the incidence of hepatocellular carcinoma (HCC) suggests an important role of estrogens in HCC pathogenesis. In this study, we conducted a case-control study to investigate whether breast cancer risk-associated single nucleotide polymorphisms (SNPs) located at estrogens loci identified by genome-wide association studies (GWASs) also predispose to HCC in a Chinese population. Three candidate SNPs at 6q25.1 were genotyped in 2,025 HCC cases and 2,032 healthy controls. Differential expression analyses and expression quantitative trait loci (eQTL) analyses were conducted to further explore the role of significant SNPs and genes they reside in...
March 3, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28333398/dietary-cholesterol-interacts-with-srebf1-to-modulate-obesity-in-chinese-children
#19
Shixiu Zhang, Xinying Lin, Henry Lynn, Guifa Xu, Jun Li, Changfeng Zhao, Mingmei Li
SCOPE: Sterol Regulatory Element Binding Protein 1 Gene (SREBF1) is an important candidate gene for obesity that could be affected by cholesterol. Different SREBF1 gene variants may have distinct responses to cholesterol, leading to different risks for obesity and obesity-related metabolic traits. Thus, we performed a gene-by-diet correlation analysis to test whether SREBF1 gene variation modulate the relationship between cholesterol and obesity. METHODS AND RESULTS: A total of 642 school-aged children in Jinan, China, were selected by stratified cluster nested sampling...
March 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28333014/single-nucleotide-polymorphism-tgf%C3%AE-1-r25p-correlates-with-acute-toxicity-during-neoadjuvant-chemoradiotherapy-in-rectal-cancer-patients
#20
J Joshua Smith, Isaac Wasserman, Sarah A Milgrom, Oliver S Chow, Chin-Tung Chen, Sujata Patil, Karyn A Goodman, Julio Garcia-Aguilar
PURPOSE: To validate the finding of an association between single nucleotide polymorphisms (SNPs) and toxicity during chemoradiotherapy (CRT) in rectal cancer patients, in an independent population. METHODS AND MATERIALS: The cohort consisted of 165 patients who received CRT for rectal cancer from 2006 to 2012. Prospectively recorded toxicity information, graded according to the Common Terminology Criteria for Adverse Events version 3.0, was retrieved from the medical record...
April 1, 2017: International Journal of Radiation Oncology, Biology, Physics
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