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Single Polymorphism Nucleotide (SNPs)

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https://www.readbyqxmd.com/read/29346564/genome-wide-comparison-of-allele-specific-gene-expression-between-african-and-european-populations
#1
Lei Tian, Asifullah Khan, Zhilin Ning, Kai Yuan, Chao Zhang, Haiyi Lou, Yuan Yuan, Shuhua Xu
Transcriptomic diversity across human populations reflects differential regulatory mechanisms. Allelic-imbalanced gene expression is a genetic regulatory mechanism that contributes to human phenotypic variation. To systematically investigate genome-wide allele-specific expression (ASE), we analyzed RNA-Seq data from European and African populations provided by the Geuvadis project. We identified 17 sites in 13 genes showing ASE in both Europeans and Africans, and 19 sites in 18 genes showing population-specific ASE, including both novel and known ASE signals...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346471/use-of-single-nucleotide-polymorphisms-and-mammographic-density-plus-classic-risk-factors-for-breast-cancer-risk-prediction
#2
Elke M van Veen, Adam R Brentnall, Helen Byers, Elaine F Harkness, Susan M Astley, Sarah Sampson, Anthony Howell, William G Newman, Jack Cuzick, D Gareth R Evans
Importance: Single-nucleotide polymorphisms (SNPs) have demonstrated an association with breast cancer susceptibility, but there is limited evidence on how to incorporate them into current breast cancer risk prediction models. Objective: To determine whether a panel of 18 SNPs (SNP18) may be used to predict breast cancer in combination with classic risk factors and mammographic density. Design, Setting, and Participants: This cohort study enrolled a subcohort of 9363 women, aged 46 to 73 years, without a previous breast cancer diagnosis from the larger prospective cohort of the PROCAS study (Predicting Risk of Cancer at Screening) specifically to evaluate breast cancer risk-assessment methods...
January 18, 2018: JAMA Oncology
https://www.readbyqxmd.com/read/29344947/genome-wide-population-structure-and-admixture-analysis-reveals-weak-differentiation-among-ugandan-goat-breeds
#3
R B Onzima, M R Upadhyay, R Mukiibi, E Kanis, M A M Groenen, R P M A Crooijmans
Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei...
January 17, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29344273/a-single-nucleotide-polymorphism-in-cyp1b1-leads-to-differential-prostate-cancer-risk-and-telomere-length
#4
Cheng-Yuan Gu, Gao-Xiang Li, Yu Zhu, Hua Xu, Yao Zhu, Xiao-Jian Qin, Dai Bo, Ding-Wei Ye
BACKGROUND: Cytochrome P450 1B1 (CYP1B1) is a key enzyme in its oestrogen metabolism pathway, giving rise to hydroxylation and conjugation. Functionally relevant genetic variants within CYP1B1 may affect the telomere length and subsequently lead to prostate carcinogenesis. METHODS: We evaluated 8 CYP1B1 tag single nucleotide polymorphisms (SNPs) in 1015 men with prostate cancer (PCa) and 1052 cancer-free controls, and calculated odds ratios (ORs) and 95% confidence intervals (CIs) to estimate their association with risk of PCa...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29344113/downregulated-mirna-1269a-variant-rs73239138-decreases-the-susceptibility-to-gastric-cancer-via-targeting-znf70
#5
Wenshuai Li, Huilu Zhang, Pei Min, Jie Zhu, Diannan Xu, Weiru Jiang, Yanyun Ma, Jigang Qiu, Weihong Xu, Jian Chen, Mingqing Zhang, Min Li, Dongqin Yang, Jianping Shi, Jun Zhang, Jie Liu
Although emerging evidence has indicated that single nucleotide polymorphisms (SNPs) in microRNAs (miRNAs) are associated with susceptibility to gastric cancer, a limited number of studies have revealed the underlying molecular mechanisms. In the present study, the results suggested that miR-1269a rs73239138 has a role in decreasing the risk of gastric cancer. The level of miR-1269a variant expression was significantly downregulated compared with the wild-type miR-1269a in the gastric cells (Fig. 1). Furthermore, overexpression of miR-1269a inhibited apoptosis of gastric cancer cells...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343654/intestinal-epithelial-cell-specific-deletion-of-%C3%AE-mannosidase-ii-ameliorates-experimental-colitis
#6
Koichiro Suzuki, Takahiro Yamada, Keiko Yamazaki, Masato Hirota, Narumi Ishihara, Mizuki Sakamoto, Daisuke Takahashi, Hideki Iijima, Koji Hase
Inflammatory bowel disease (IBD) is a refractory disease of the gastrointestinal tract that is believed to develop in genetically susceptible individuals. Glycosylation, a type of post-translational modification, is involved in the development of a wide range of diseases, including IBD, by modulating the function of various glycoproteins. To identify novel genes contributing to the development of IBD, we analyzed single nucleotide polymorphisms (SNPs) of glycosylation-related genes in IBD patients and identified MAN2A1, encoding alpha-mannosidase II (α-MII), as a candidate gene...
January 18, 2018: Cell Structure and Function
https://www.readbyqxmd.com/read/29343214/establishing-a-genetic-link-between-fto-and-vdr-gene-polymorphisms-and-obesity-in-the-emirati-population
#7
Saad Mahmud Khan, Sarah El Hajj Chehadeh, Mehera Abdulrahman, Wael Osman, Habiba Al Safar
BACKGROUND: Obesity is a metabolic disease that is widely prevalent with approximately 600 million people classified as obese worldwide. Its etiology is multifactorial and involves a complex interplay between genes and the environment. Over the past few decades, obesity rates among the Emirati population have been increasing. The aim of this study was to investigate the association of candidate gene single nucleotide polymorphisms (SNPs), namely FTO (rs9939609) and VDR (rs1544410), with obesity in the UAE population...
January 17, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29342889/a-case-control-study-of-the-genetic-variability-in-reactive-oxygen-species-metabolizing-enzymes-in-melanoma-risk
#8
Tze-An Yuan, Vandy Yourk, Ali Farhat, Argyrios Ziogas, Frank L Meyskens, Hoda Anton-Culver, Feng Liu-Smith
Recent studies have shown that ultraviolet (UV)-induced chemiexcitation of melanin fragments leads to DNA damage; and chemiexcitation of melanin fragments requires reactive oxygen species (ROS), as ROS excite an electron in the melanin fragments. In addition, ROS also cause DNA damages on their own. We hypothesized that ROS producing and metabolizing enzymes were major contributors in UV-driven melanomas. In this case-control study of 349 participants, we genotyped 23 prioritized single nucleotide polymorphisms (SNPs) in nicotinamide adenine dinucleotide phosphate (NADPH) oxidases 1 and 4 (NOX1 and NOX4, respectively), CYBA, RAC1, superoxide dismutases (SOD1, SOD2, and SOD3) and catalase (CAT), and analyzed their associated melanoma risk...
January 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29341862/identification-of-three-genetic-variants-as-novel-susceptibility-loci-for-body-mass-index-in-a-japanese-population
#9
Yoshiki Yasukochi, Jun Sakuma, Ichiro Takeuchi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Yoshiji Yamada
Recent genome-wide association studies have identified various obesity or metabolic syndrome (MetS) susceptibility loci. However, most studies were conducted in a cross-sectional manner. To address this gap, we performed a longitudinal exome-wide association study to identify susceptibility loci for obesity and MetS in a Japanese population. We traced clinical data of 6022 Japanese who had annual health check-ups for several years (mean follow-up period, 5 years), and genotyped ~244,000 genetic variants. The association of single nucleotide polymorphisms (SNPs) with body mass index (BMI) or the prevalence of obesity and MetS was examined using a generalized estimating equation model...
January 12, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29341488/gene-gene-interaction-between-msx1-and-tp63-in-asian-case-parent-trios-with-nonsyndromic-cleft-lip-with-or-without-cleft-palate
#10
Dongjing Liu, Holger Schwender, Mengying Wang, Hong Wang, Ping Wang, Hongping Zhu, Zhibo Zhou, Jing Li, Tao Wu, Terri H Beaty
BACKGROUND: Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P)...
January 17, 2018: Birth Defects Research
https://www.readbyqxmd.com/read/29340898/epidemiological-aspects-of-healthcare-associated-infections-and-microbial-genomics
#11
C Mirande, I Bizine, A Giannetti, N Picot, A van Belkum
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO)...
January 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29340614/association-of-polygenic-risk-score-with-cognitive-decline-and-motor-progression-in-parkinson-disease
#12
Kimberly C Paul, Jessica Schulz, Jeff M Bronstein, Christina M Lill, Beate R Ritz
Importance: Genetic factors have a well-known influence on Parkinson disease (PD) susceptibility. The largest genome-wide association study (GWAS) identified 26 independent single-nucleotide polymorphisms (SNPs) associated with PD risk. Among patients, the course and severity of symptom progression is variable, and little is known about the potential association of genetic factors with phenotypic variance. Objective: To assess whether GWAS-identified PD risk SNPs also have a cumulative association with the progression of cognitive and motor symptoms in patients with PD...
January 16, 2018: JAMA Neurology
https://www.readbyqxmd.com/read/29340108/effect-of-gene-lifestyle-interaction-on-gestational-diabetes-risk
#13
Polina V Popova, Alexandra A Klyushina, Lyudmila B Vasilyeva, Alexandra S Tkachuk, Yana A Bolotko, Andrey S Gerasimov, Evgenii A Pustozerov, Ekaterina N Kravchuk, Alexander Predeus, Anna A Kostareva, Elena N Grineva
We hypothesized that the association of certain lifestyle parameters with gestational diabetes mellitus (GDM) risk would depend on susceptibility loci. In total, 278 Russian women with GDM and 179 controls completed questionnaires about lifestyle habits (food consumption, physical activity and smoking). GDM was diagnosed according to the criteria of the International Association of Diabetes and Pregnancy Study Groups. Maternal blood was sampled for genotyping single-nucleotide polymorphisms (SNPs) in MTNR1B (rs10830963 and rs1387153), GCK (rs1799884), KCNJ11 (rs5219), IGF2BP2 (rs4402960), TCF7L2 (rs7903146 and rs12255372), CDKAL1 (rs7754840), IRS1 (rs1801278) and FTO (rs9939609)...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340069/methylenetetrahydrofolate-reductase-tagging-polymorphisms-are-associated-with-risk-of-esophagogastric-junction-adenocarcinoma-a-case-control-study-involving-2-740-chinese-han-subjects
#14
Guowen Ding, Yafeng Wang, Yu Chen, Jun Yin, Chao Liu, Yu Fan, Hao Qiu, Weifeng Tang, Shuchen Chen
In this study, we aimed to determine the potential association of MTHFR tagging single nucleotide polymorphisms (SNPs) with risk of developing esophagogastric junction adenocarcinoma (EGJA). MTHFR rs1801133 G>A, rs3753584 T>C, rs4845882 G>A, rs4846048 A>G and rs9651118 T>C polymorphisms were genotyped in 1,677 healthy individuals and 1,063 patients with EGJA. We found that MTHFR rs1801133 G>A polymorphism was significantly associated with the risk of developing EGJA (AA vs. GG: adjusted P = 0...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340035/abcb1-3435tt-and-abcg2-421cc-genotypes-were-significantly-associated-with-longer-progression-free-survival-in-chinese-breast-cancer-patients
#15
Wanjun Li, Dan Zhang, Fen Du, Xuemei Xing, Ying Wu, Dong Xiao, Ming Liang, Zhigang Fan, Peng Zhao, Tao Liu, Guoyin Li
Objective: To investigate the distribution of ABCB1 C3435T and ABCG2 C421A gene polymorphisms in Chinese Han population and their influences on the susceptibility and prognosis of breast carcinoma. Methods: A total of 200 female subjects were enrolled in this study, comprising 100 breast cancer patients and 100 healthy controls. Carcinoma and para-carcinoma tissues were collected from the breast cancer patients, while peripheral blood was collected from healthy controls...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340022/a-functional-polymorphism-of-ssbp1-gene-predicts-prognosis-and-response-to-chemotherapy-in-resected-gastric-cancer-patients
#16
Qiuchen Li, Falin Qu, Renli Li, Xianli He, Yulong Zhai, Weigang Chen, Yong Zheng
Growing evidence has indicated that single-stranded DNA-binding proteins 1 (SSBP1) is involved in tumor initiation and progression. However, effects of single nucleotide polymorphisms (SNPs) in SSBP1 gene on gastric cancer (GC) prognosis are still unknown. In present study, two functional SNPs from SSBP1 were selected and genotyped in a large cohorts of 1030 resected GC patients (326 in the training set, 704 in the validation set) to explore the association of SNPs with patients' survival. The rs6976500 G allele (CG/GG) genotypes were found significantly associated with both worse overall survival (OS) and recurrence-free survival (RFS) in the training and the independent validation set when compared to C allele genotype, which reaching a more robust statistical significance in the pooled analysis...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339533/learning-dependent-chromatin-remodeling-highlights-noncoding-regulatory-regions-linked-to-autism
#17
John N Koberstein, Shane G Poplawski, Mathieu E Wimmer, Giulia Porcari, Charlly Kao, Bruce Gomes, Davide Risso, Hakon Hakonarson, Nancy R Zhang, Robert T Schultz, Ted Abel, Lucia Peixoto
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder that is associated with genetic risk factors. Most human disease-associated single-nucleotide polymorphisms (SNPs) are not located in genes but rather are in regulatory regions that control gene expression. The function of regulatory regions is determined through epigenetic mechanisms. Parallels between the cellular basis of development and the formation of long-term memory have long been recognized, particularly the role of epigenetic mechanisms in both processes...
January 16, 2018: Science Signaling
https://www.readbyqxmd.com/read/29338921/faster-progression-from-mci-to-probable-ad-for-carriers-of-a-single-nucleotide-polymorphism-associated-with-type-2-diabetes
#18
Hugo Girard, Olivier Potvin, Scott Nugent, Caroline Dallaire-Théroux, Stephen Cunnane, Simon Duchesne
Sporadic Alzheimer's disease (AD), as opposed to its autosomal dominant form, is likely caused by a complex interaction of genetic, environmental, and health lifestyle factors. Twin studies indicate that sporadic AD heritability could be between 58% and 79%, around half of which is explained by the ε4 allele of the apolipoprotein E (APOE4). We hypothesized that genes associated with known risk factors for AD, namely hypertension, hypercholesterolemia, obesity, diabetes, and cardiovascular disease, would contribute significantly to the remaining heritability...
December 7, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29338687/use-of-easy-measurable-phenotypic-traits-as-a-complementary-approach-to-evaluate-the-population-structure-and-diversity-in-a-high-heterozygous-panel-of-tetraploid-clones-and-cultivars
#19
Martin E Tagliotti, Sofia I Deperi, Maria C Bedogni, Ruofang Zhang, Norma C Manrique Carpintero, Joseph Coombs, David Douches, Marcelo A Huarte
BACKGROUND: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs...
January 16, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29338330/joint-influence-of-snps-and-dna-methylation-on-lipids-in-african-americans-from-hypertensive-sibships
#20
Michelle L Wright, Erin B Ware, Jennifer A Smith, Sharon L R Kardia, Jacquelyn Y Taylor
INTRODUCTION: Plasma concentrations of lipids (i.e., total cholesterol, high-density cholesterol, low-density cholesterol, and triglycerides) are amenable to therapeutic intervention and remain important factors for assessing risk of cardiovascular diseases. Some of the observed variability in serum lipid concentrations has been associated with genetic and epigenetic variants among cohorts with European ancestry (EA). Serum lipid levels have also been associated with genetic variants in multiethnic populations...
January 1, 2018: Biological Research for Nursing
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