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Single nucleotide polymorphisms (SNPs)

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https://www.readbyqxmd.com/read/29352395/association-between-crp-genetic-diversity-and-bipolar-disorder-comorbid-complications
#1
Wahid Boukouaci, José Oliveira, Bruno Etain, Meriem Bennabi, Christina Mariaselvam, Nora Hamdani, Céline Manier, Djaouida Bengoufa, Frank Bellivier, Chantal Henry, Jean-Pierre Kahn, Dominique Charron, Rajagopal Krishnamoorthy, Marion Leboyer, Ryad Tamouza
BACKGROUND: Chronic low-grade inflammation is believed to contribute, at least in a subset of patients, to the development of bipolar disorder (BD). In this context, the most investigated biological marker is the acute phase response molecule, C-reactive protein (CRP). While the genetic diversity of CRP was amply studied in various pathological settings, little is known in BD. METHODS: 568 BD patients along with 163 healthy controls (HC) were genotyped for the following single-nucleotide polymorphisms (SNPs) on the CRP gene: intron rs1417938 (+ 29) T/A, 3'-UTR rs1130864 (+ 1444) G/A, and downstream rs1205 (+ 1846) (C/T)...
January 20, 2018: International Journal of Bipolar Disorders
https://www.readbyqxmd.com/read/29352323/identification-of-a-molecular-marker-tightly-linked-to-bacterial-wilt-resistance-in-tomato-by-genome-wide-snp-analysis
#2
Boyoung Kim, In Sun Hwang, Hyung Jin Lee, Je Min Lee, Eunyoung Seo, Doil Choi, Chang-Sik Oh
Genotyping of disease resistance to bacterial wilt in tomato by a genome-wide SNP analysis Bacterial wilt caused by Ralstonia pseudosolanacearum is one of the destructive diseases in tomato. The previous studies have identified Bwr-6 (chromosome 6) and Bwr-12 (chromosome 12) loci as the major quantitative trait loci (QTLs) contributing to resistance against bacterial wilt in tomato cultivar 'Hawaii7996'. However, the genetic identities of two QTLs have not been uncovered yet. In this study, using whole-genome resequencing, we analyzed genome-wide single-nucleotide polymorphisms (SNPs) that can distinguish a resistant group, including seven tomato varieties resistant to bacterial wilt, from a susceptible group, including two susceptible to the same disease...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29352099/smoking-and-parkinson-disease-evidence-for-gene-by-smoking-interactions
#3
Pei-Chen Lee, Ismaïl Ahmed, Marie-Anne Loriot, Claire Mulot, Kimberly C Paul, Jeff M Bronstein, Beate Ritz, Alexis Elbaz
OBJECTIVE: To investigate whether cigarette smoking interacts with genes involved in individual susceptibility to xenobiotics for the risk of Parkinson disease (PD). METHODS: Two French population-based case-control studies (513 patients, 1,147 controls) were included as a discovery sample to examine gene-smoking interactions based on 3,179 single nucleotide polymorphisms (SNPs) in 289 genes involved in individual susceptibility to xenobiotics. SNP-by-cigarette smoking interactions were tested in the discovery sample through an empirical Bayes (EB) approach...
January 19, 2018: Neurology
https://www.readbyqxmd.com/read/29352079/identification-and-validation-of-a-new-source-of-low-grain-cadmium-accumulation-in-durum-wheat
#4
Atena Oladzad Abbasabadi, Ajay Kumar, Seyed Pirseyedi, Evan Salsman, Marina Dobrydina, Roshan Sharma Poudel, Wesam A AbuHammad, Shiaoman Chao, Justin D Faris, Elias M Elias
Cadmium (Cd) is a heavy metal that has no known biological function and is toxic for many living organisms. The maximum level of Cd concentration allowed in the international market for wheat grain is 0.2 mg kg-1. Because phenotyping for Cd uptake is expensive and time consuming, molecular markers associated with genes conferring low Cd uptake would expedite selection and lead to the development of durum cultivars with reduced Cd concentrations. Here, we identified single nucleotide polymorphisms (SNPs) associated with a novel low Cd uptake locus in the durum experimental line D041735, which has hexaploid common wheat in its pedigree...
January 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29351800/drug-resistance-genes-pvcrt-o-and-pvmdr-1-polymorphism-in-patients-from-malaria-endemic-south-western-coastal-region-of-india
#5
Shiny Joy, Benudhar Mukhi, Susanta K Ghosh, Rajeshwara N Achur, D Channe Gowda, Namita Surolia
BACKGROUND: Malaria is highly prevalent in many parts of India and is mostly caused by the parasite species Plasmodium vivax followed by Plasmodium falciparum. Chloroquine (CQ) is the first-line treatment for blood stage P. vivax parasites, but cases of drug resistance to CQ have been reported from India. One of the surveillance strategies which is used to monitor CQ drug resistance, is the analysis of single nucleotide polymorphisms (SNPs) of the associated gene markers. Susceptibility to CQ can also be determined by copy number assessment of multidrug resistant gene (mdr-1)...
January 19, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29351603/the-unexpected-function-of-a-flavin-dependent-oxidoreductase-fox-from-variovorax-paradoxus-tbea6
#6
Christina Meinert, Marc Schürmann, Jan-Eike Domeyer, Anja Poehlein, Rolf Daniel, Alexander Steinbüchel
3,3'-Thiodipropionic acid (TDP) is used as an additive in food and cosmetic industry and as precursor substrate for biotechnical polythioester production. Its catabolism was investigated in Variovorax paradoxus TBEA6 previous to this study. It was reported that the insertion of the transposon Tn5::mob into a gene showing high homology to flavin-dependent oxidoreductases (fox) resulted in impaired growth with TDP. Therefore, it was assumed that the initial cleavage of TDP is catalyzed by an FAD-dependent oxidoreductase (Fox, VPARA_05580)...
January 17, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29349811/genetic-analysis-of-interleukin-18-gene-polymorphisms-in-alopecia-areata
#7
Sumeyya Deniz Celik, Omer Ates
BACKGROUND: Alopecia areata (AA), which appears as nonscarring hair shedding on any hair-bearing area, is a common organ-specific autoimmune condition. Cytokines have important roles in the development of AA. Interleukin (IL) 18 is a significant proinflammatory cytokine that was found higher in the patients with AA. We aimed to investigate whether the IL-18 (rs187238 and rs1946518) single nucleotide polymorphisms (SNPs) may be associated with AA and/or clinical outcome of patients with AA in Turkish population...
January 18, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29348888/the-association-analysis-of-tlr2-and-tlr4-gene-with-tuberculosis-in-the-tibetan-chinese-population
#8
Xin Xue, Yi Qiu, Dong Jiang, Tianbo Jin, Mengdan Yan, Xikang Zhu, Yonglie Chu
Background: The present study was undertaken to explore the relationship of Toll-like receptor (TLR) 2, TLR4 genes polymorphisms with Pulmonary tuberculosis (PTB) risk in a sample of Chinese population. Methods: For this study, we recruited 467 subjects with PTB and 504 healthy subjects from a Tibetan population living in near or in Xi'an, China. Association analyses of single-nucleotide polymorphisms (SNPs) in TLR2 and TLR4 were performed with SPSS Statistics (version 17...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348838/single-nucleotide-polymorphisms-in-znf208-are-associated-with-increased-risk-for-hbv-in-chinese-people
#9
Hengxin Li, Jun Chen, RuiZhi Zhang, Ran Xu, Zhe Zhang, Le Ren, Qi Yang, Yumei Tian, Daxu Li
Single nucleotide polymorphisms (SNPs) in ZNF208 may be associated with susceptibility to Hepatitis B virus (HBV). In the current study, we analyzed the association between ZNF208 SNPs and risk of HBV in 242 HBV patients and 300 healthy subjects from the Xi'an area of Chinese Han Population. Of the five SNPs examined, rs2188971 (OR: 1.36, 95% CI: 1.04-1.76, P = 0.022), rs8103163 (OR: 1.40, 95% CI: 1.08-1.82, P = 0.010) and rs7248488 (OR: 1.38, 95% CI: 1.07-1.79, P = 0.014) were correlated with HBV susceptibility based on Chi-square tests...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348692/genome-wide-search-for-higher-order-epistasis-as-modifiers-of-treatment-effects-on-bone-mineral-density-in-childhood-cancer-survivors
#10
Cindy Im, Kirsten K Ness, Sue C Kaste, Wassim Chemaitilly, Wonjong Moon, Yadav Sapkota, Russell J Brooke, Melissa M Hudson, Leslie L Robison, Yutaka Yasui, Carmen L Wilson
Single-nucleotide polymorphisms (SNPs) contributing to interactions between regulatory elements that modulate gene transcription may explain some of the uncharacterized variation for complex traits. We explored this hypothesis among 856 adult survivors of pediatric cancer exposed to curative treatments that adversely affect bone mineral density (BMD). To restrict our search to interactions among SNPs in regulatory elements, our analysis considered 75523 SNPs mapped to putative promoter or enhancer regions. In anticipation that power to detect higher order epistasis would be low using an exhaustive search and a Bonferroni-corrected threshold for genome-wide significance (e...
January 18, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29348398/association-study-of-polymorphisms-in-genes-relevant-to-vitamin-b12-and-folate-metabolism-with-childhood-autism-spectrum-disorder-in-a-han-chinese-population
#11
Zengyu Zhang, Lianfang Yu, Sufang Li, Jun Liu
BACKGROUND Both genetic and environmental factors play a role in the development of autism spectrum disorder (ASD). This case-control study examined the association between childhood ASD and single-nucleotide polymorphisms (SNPs) in genes involved with vitamin B12 and folate metabolism. MATERIAL AND METHODS Genotypes of transcobalamin 2 (TCN2) rs1801198, methionine synthase (MTR) rs1805087, methionine synthase reductase (MTRR) rs1801394, and methylene tetrahydrofolate reductase (MTHFR) rs1801133 were examined in 201 children with ASD and 200 healthy controls from the Han Chinese population...
January 19, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29346564/genome-wide-comparison-of-allele-specific-gene-expression-between-african-and-european-populations
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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