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Single nucleotide polymorphism

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https://www.readbyqxmd.com/read/28647964/-association-between-single-nucleotide-polymorphism-of-bard1-gene-and-brca1-gene-mutation-in-epithelial-ovarian-cancer
#1
W L Liu, J Z Zhao, Z Z Wang, B Dong, Y Y Hou, X X Wu, Y J Guo
Objective: To investigate the relationship between single nucleotide polymorphism (SNP) of BARD1 gene and BRCA1 gene in epithelial ovarian cancer (EOC). Methods: Nineteen EOC patients with BRCA1 gene mutation and 50 EOC cases without BRCA1 gene mutation between January 2016 and October 2016 were collected, and all EOC were diagnosed by pathological method. BARD1 gene variants were detected by next generation sequencing (NGS). The SNP of BARD1 gene was analyzed by Pearson linear correlation. Logistic regression analysis was used to research the clinicopathologic features and BRCA1 gene mutation associated with BARD1 gene SNP...
June 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28647900/breast-cancer-risk-associated-with-genotype-polymorphisms-of-the-aurora-kinase-a-gene-aurka-a-case-control-study-in-a-high-altitude-ecuadorian-mestizo-population
#2
Andrés López-Cortés, Alejandro Cabrera-Andrade, Fabián Oña-Cisneros, Felipe Rosales, Malena Ortiz, Eduardo Tejera, César Paz-Y-Miño
Breast cancer (BC) is the leading cause of cancer related death among women in 2014. The AURKA gene that encodes the protein called Aurora kinase A plays an important role in the progression of the cell cycle, by controlling and promoting the entry into the phase of mitosis. The single nucleotide polymorphism AURKA T91A (rs2273535) (Phe21Ile) has been identified as functional alternator of this kinase, the Ile allele is associated with the occurrence of chromosome segregation errors and tumor progression. Therefore, it is essential to know how BC risk is associated with histopathological characteristics, immunohistochemical characteristics, and genotype polymorphism in a high altitude Ecuadorian mestizo population...
June 24, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28647682/body-mass-index-body-dissatisfaction-and-adolescent-smoking-initiation
#3
Laurence J Howe, Lea Trela-Larsen, Michelle Taylor, Jon Heron, Marcus R Munafò, Amy E Taylor
BACKGROUND: Smoking influences body weight, but there is little evidence as to whether body mass index (BMI) and body dissatisfaction increase smoking initiation in adolescents. METHODS: We evaluated the association between measured BMI, body dissatisfaction and latent classes of smoking initiation (never smokers, experimenters, late onset regular smokers, early onset regular smokers) in the Avon Longitudinal Study of Parents and Children. In observational analyses we used BMI (N=3754) and body dissatisfaction at age 10...
June 8, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/28647327/genomic-analysis-of-cow-mortality-and-milk-production-using-a-threshold-linear-model
#4
S Tsuruta, D A L Lourenco, I Misztal, T J Lawlor
The objective of this study was to investigate the feasibility of genomic evaluation for cow mortality and milk production using a single-step methodology. Genomic relationships between cow mortality and milk production were also analyzed. Data included 883,887 (866,700) first-parity, 733,904 (711,211) second-parity, and 516,256 (492,026) third-parity records on cow mortality (305-d milk yields) of Holsteins from Northeast states in the United States. The pedigree consisted of up to 1,690,481 animals including 34,481 bulls genotyped with 36,951 SNP markers...
June 21, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28646884/the-increased-concentration-of-macrophage-migration-inhibitory-factor-in-serum-and-cerebrospinal-fluid-of-patients-with-tick-borne-encephalitis
#5
Sambor Grygorczuk, Miłosz Parczewski, Renata Świerzbińska, Piotr Czupryna, Anna Moniuszko, Justyna Dunaj, Maciej Kondrusik, Sławomir Pancewicz
BACKGROUND: Host factors determining the clinical presentation of tick-borne encephalitis (TBE) are not fully elucidated. The peripheral inflammatory response to TBE virus is hypothesized to facilitate its entry into central nervous system by disrupting the blood-brain barrier with the involvement of a signaling route including Toll-like receptor 3 (TLR3) and pro-inflammatory cytokines macrophage migration inhibitory factor (MIF), tumor necrosis factor-α (TNFα), and interleukin-1 beta (IL-1β)...
June 24, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28645331/circadian-clock-gene-polymorphisms-in-relation-to-sleep-patterns-and-obesity-in-african-americans-findings-from-the-jackson-heart-study
#6
Pia Riestra, Samson Y Gebreab, Ruihua Xu, Rumana J Khan, Amadou Gaye, Adolfo Correa, Nancy Min, Mario Sims, Sharon K Davis
BACKGROUND: Circadian rhythms regulate key biological processes and the dysregulation of the intrinsic clock mechanism affects sleep patterns and obesity onset. The CLOCK (circadian locomotor output cycles protein kaput) gene encodes a core transcription factor of the molecular circadian clock influencing diverse metabolic pathways, including glucose and lipid homeostasis. The primary objective of this study was to evaluate the associations between CLOCK single nucleotide polymorphisms (SNPs) and body mass index (BMI)...
June 23, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28644843/a-high-density-genetic-map-and-qtl-analysis-of-agronomic-traits-in-foxtail-millet-setaria-italica-l-p-beauv-using-rad-seq
#7
Jun Wang, Zhilan Wang, Xiaofen Du, Huiqing Yang, Fang Han, Yuanhuai Han, Feng Yuan, Linyi Zhang, Shuzhong Peng, Erhu Guo
Foxtail millet (Setaria italica), a very important grain crop in China, has become a new model plant for cereal crops and biofuel grasses. Although its reference genome sequence was released recently, quantitative trait loci (QTLs) controlling complex agronomic traits remains limited. The development of massively parallel genotyping methods and next-generation sequencing technologies provides an excellent opportunity for developing single-nucleotide polymorphisms (SNPs) for linkage map construction and QTL analysis of complex quantitative traits...
2017: PloS One
https://www.readbyqxmd.com/read/28644774/cd33-splicing-polymorphism-determines-gemtuzumab-ozogamicin-response-in-de-novo-acute-myeloid-leukemia-report-from-randomized-phase-iii-children-s-oncology-group-trial-aaml0531
#8
Jatinder K Lamba, Lata Chauhan, Miyoung Shin, Michael R Loken, Jessica A Pollard, Yi-Cheng Wang, Rhonda E Ries, Richard Aplenc, Betsy A Hirsch, Susana C Raimondi, Roland B Walter, Irwin D Bernstein, Alan S Gamis, Todd A Alonzo, Soheil Meshinchi
Purpose Gemtuzumab ozogamicin (GO), a CD33-targeted immunoconjugate, is a re-emerging therapy for acute myeloid leukemia (AML). CD33 single nucleotide polymorphism rs12459419 C>T in the splice enhancer region regulates the expression of an alternatively spliced CD33 isoform lacking exon2 (D2-CD33), thus eliminating the CD33 IgV domain, which is the antibody-binding site for GO, as well as diagnostic immunophenotypic panels. We aimed to determine the impact of the genotype of this splicing polymorphism in patients with AML treated with GO-containing chemotherapy...
June 23, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28644415/genome-wide-association-study-of-dietary-pattern-scores
#9
Frédéric Guénard, Annie Bouchard-Mercier, Iwona Rudkowska, Simone Lemieux, Patrick Couture, Marie-Claude Vohl
Dietary patterns, representing global food supplies rather than specific nutrients or food intakes, have been associated with cardiovascular disease (CVD) incidence and mortality. The contribution of genetic factors in the determination of food intakes, preferences and dietary patterns has been previously established. The current study aimed to identify novel genetic factors associated with reported dietary pattern scores. Reported dietary patterns scores were derived from reported dietary intakes for the preceding month and were obtained through a food frequency questionnaire and genome-wide association study (GWAS) conducted in a study sample of 141 individuals...
June 23, 2017: Nutrients
https://www.readbyqxmd.com/read/28644142/acyp2-polymorphisms-are-associated-with-the-risk-of-liver-cancer-in-a-han-chinese-population
#10
Zhong Chen, Yu Sun, Zhenxiong Xu, Junnv Xu, Jingjie Li, Mengdan Yan, Jing Li, Tianbo Jin, Haifeng Lin
We explored the association between single nucleotide polymorphisms (SNPs) in ACYP2 and liver cancer risk. Thirteen SNPs were genotyped in 473 cases and 564 controls. Genetic model, linkage disequilibrium, and haplotype analyses were performed to evaluate the association between ACPY2 SNPs and liver cancer risk. We found that rs6713088 (G allele: odds ratio [OR] = 1.27, 95% confidence interval [CI]: 1.07-1.52, P = 0.007; GG vs. CC: OR = 1.49, 95% CI: 1.02-2.1, P = 0.038), rs843711 (T allele: OR = 1.29, 95% CI: 1...
June 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644130/mmp-3-gene-polymorphisms-are-associated-with-increased-risk-of-osteoarthritis-in-chinese-men
#11
Wen Guo, Pengcheng Xu, Tianbo Jin, Jihong Wang, Dongsheng Fan, Zengtao Hao, Yuntao Ji, Shangfei Jing, Chaoqian Han, Jieli Du, Dong Jiang, Shuzheng Wen, Jianzhong Wang
Osteoarthritis (OA) is the most common late-onset degenerative joint disease., It is characterized by progressive degradation of articular cartilage. We investigated the association between OA occurrence and single nucleotide polymorphisms (SNPs) in the matrix metalloproteinase-3 (MMP-3)gene involved in the breakdown of extra-cellular matrix proteins. The study included 100 male OA patients and 197 healthy men from the north area of China. Eight MMP-3 SNPs were genotyped. Odds ratios (ORs) with 95% confidence intervals (95%CIs) and multivariate logistic regression analysis were used to assess the association...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643617/preselection-statistics-and-random-forest-classification-identify-population-informative-single-nucleotide-polymorphisms-in-cosmopolitan-and-autochthonous-cattle-breeds
#12
F Bertolini, G Galimberti, G Schiavo, S Mastrangelo, R Di Gerlando, M G Strillacci, A Bagnato, B Portolano, L Fontanesi
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna)...
June 23, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28642860/ataxia-telangiectasia-mutated-atm-polymorphisms-and-risk-of-lung-cancer-in-a-chinese-population
#13
Ajay A Myneni, Shen-Chih Chang, Rungui Niu, Li Liu, Baoxing Zhao, Jianping Shi, Xiaoyou Han, Jiawei Li, Jia Su, Shunzhang Yu, Zuo-Feng Zhang, Lina Mu
BACKGROUND: The ataxia telangiectasia-mutated (ATM) gene has a key role in DNA repair including activation and stabilization of p53, which implicates the importance of ATM polymorphisms in the development of cancer. This study aims to investigate the association of two ATM single-nucleotide polymorphisms (SNPs) with lung cancer, as well as their potential interaction with p53 gene and other known risk factors of lung cancer. METHODS: A population-based case-control study was conducted in Taiyuan city, China with 399 cases and 466 controls matched on the distribution of age and sex of cases...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28642764/xylella-fastidiosa-host-range-and-advance-in-molecular-identification-techniques
#14
REVIEW
Paolo Baldi, Nicola La Porta
In the never ending struggle against plant pathogenic bacteria, a major goal is the early identification and classification of infecting microorganisms. Xylella fastidiosa, a Gram-negative bacterium belonging to the family Xanthmonadaceae, is no exception as this pathogen showed a broad range of vectors and host plants, many of which may carry the pathogen for a long time without showing any symptom. Till the last years, most of the diseases caused by X. fastidiosa have been reported from North and South America, but recently a widespread infection of olive quick decline syndrome caused by this fastidious pathogen appeared in Apulia (south-eastern Italy), and several cases of X...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642124/identification-of-genetic-variants-associated-with-huntington-s-disease-progression-a-genome-wide-association-study
#15
Davina J Hensman Moss, Antonio F Pardiñas, Douglas Langbehn, Kitty Lo, Blair R Leavitt, Raymund Roos, Alexandra Durr, Simon Mead, Peter Holmans, Lesley Jones, Sarah J Tabrizi
BACKGROUND: Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. METHODS: We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008-11)...
June 19, 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28641921/genome-wide-association-and-interaction-studies-of-csf-t-tau-a%C3%AE-42-ratio-in-adni-cohort
#16
Jin Li, Qiushi Zhang, Feng Chen, Xianglian Meng, Wenjie Liu, Dandan Chen, Jingwen Yan, Sungeun Kim, Lei Wang, Weixing Feng, Andrew J Saykin, Hong Liang, Li Shen
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability"...
May 15, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28641622/-variation-of-lnk-gene-in-chronic-myeloid-leukemia
#17
Mei Tan, Ying Rong, Run-Mei Tian, Yu-Hang Zhu, Ping Zhu, Yan Chen
OBJECTIVE: To compare the mutation and single nucleotide polymorphism (SNP) of LNK gene between chronic myeloid leukemia(CML) and control groups, and to explore the relationship between LNK gene variation and the occurrence of CML. METHODS: A total of 36 patients with CML were selected, 46 healthy persons were used as normal controls. DNA was extracted from bone marrow and peripheral blood, BCR/ABL1 fusion gene was detected by Q-PCR. The whole exon of LNK gene was amplified by PCR...
June 2017: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/28641521/lncrna-hotair-polymorphisms-association-with-cancer-susceptibility-in-different-tumor-types
#18
Gerardo Botti, Francesca Collina, Giosuè Scognamiglio, Gabriella Aquino, Margherita Cerrone, Giuseppina Liguori, Vincenzo Gigantino, Maria Gabriella Malzone, Monica Cantile
Single nucleotide polymorphisms (SNPs) in non coding RNAs (ncRNA) molecules affect gene and protein expression and generate genetic variability influencing the risk of tumor diseases. HOTAIR is locates at the heart of the cell memory gene program and represents a prototype of long non coding RNA (LncRNA) due to its capacity to regulate in-trans a distant chromosome landscape. Aberrant expression of HOTAIR is frequently associated with pathogenesis and mostly with metastatic progression of several human cancers...
June 21, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28640939/global-transcriptome-and-co-expression-network-analyses-reveal-cultivar-specific-molecular-signatures-associated-with-seed-development-and-seed-size-weight-determination-in-chickpea
#19
Rohini Garg, Vikash K Singh, Mohan Singh Rajkumar, Vinay Kumar, Mukesh Jain
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes. About one-fourth of total genes exhibited significant differential expression in JGK 3 as compared to Himchana 1...
June 22, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28640841/a-sorghum-sorghum-bicolor-mutant-with-altered-carbon-isotope-ratio
#20
Govinda Rizal, Shanta Karki, Vivek Thakur, Samart Wanchana, Hugo Alonso-Cantabrana, Jacque Dionora, John E Sheehy, Robert Furbank, Susanne von Caemmerer, William Paul Quick
Recent efforts to engineer C4 photosynthetic traits into C3 plants such as rice demand an understanding of the genetic elements that enable C4 plants to outperform C3 plants. As a part of the C4 Rice Consortium's efforts to identify genes needed to support C4 photosynthesis, EMS mutagenized sorghum populations were generated and screened to identify genes that cause a loss of C4 function. Stable carbon isotope ratio (δ13C) of leaf dry matter has been used to distinguishspecies with C3 and C4 photosynthetic pathways...
2017: PloS One
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