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https://www.readbyqxmd.com/read/27926584/common-single-nucleotide-polymorphisms-in-transient-receptor-potential-melastatin-type-6-increase-the-risk-for-proton-pump-inhibitor-induced-hypomagnesemia-a-case-control-study
#1
Mark W Hess, Jeroen H F de Baaij, Mark M T J Broekman, Tanya M Bisseling, Bertram J T Haarhuis, Adriaan C I T L Tan, René H M Te Morsche, Joost G J Hoenderop, René J M Bindels, Joost P H Drenth
OBJECTIVE: Proton pump inhibitors (PPIs) are effective drugs for the treatment of gastric acid-related disorders. Serious adverse events are rare for PPIs, but recent data suggest that PPIs cause hypomagnesemia. The aim of this study was to estimate the frequency of PPI-induced hypomagnesemia and to define the risk factors for its development. MATERIALS AND METHODS: A total of 133 chronic users of PPIs were enrolled and patients were distinguished on the basis of their serum Mg concentrations...
December 6, 2016: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/27926379/a-comparative-analysis-of-chaotic-particle-swarm-optimizations-for-detecting-single-nucleotide-polymorphism-barcodes
#2
Li-Yeh Chuang, Sin-Hua Moi, Yu-Da Lin, Cheng-Hong Yang
OBJECTIVE: Evolutionary algorithms could overcome the computational limitations for the statistical evaluation of large datasets for high-order single nucleotide polymorphism (SNP) barcodes. Previous studies have proposed several chaotic particle swarm optimization (CPSO) methods to detect SNP barcodes for disease analysis (e.g., for breast cancer and chronic diseases). This work evaluated additional chaotic maps combined with the particle swarm optimization (PSO) method to detect SNP barcodes using a high-dimensional dataset...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27925593/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#3
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27925431/diabetes-mellitus-superoxide-dismutase-and-peroxisome-proliferator-activated-receptor-gamma-polymorphisms-modify-the-outcome-of-end-stage-renal-disease-patients-of-han-chinese-origin
#4
Chia-Ter Chao, Jenq-Wen Huang, Chih-Kang Chiang, Yen-Ching Chen, Cheng-Chung Fang, Fu-Chang Hu, Chen-Chih Chang, Chung-Jen Yen
BACKGROUND: Increased oxidative stress significantly modifies the outcome of patients with diabetes mellitus (DM) and end-stage renal disease (ESRD), and is counteracted by anti-oxidative capacity. However, whether anti-oxidant single nucleotide polymorphisms (SNPs) influence the outcome of ESRD individuals with or without DM has not been tested before. METHODS: We prospectively enrolled multi-center ESRD patients of Han Chinese origin betwen 2002 and 2003, recording their anti-oxidant (superoxide dismutase [SOD2], glutathione peroxidase [GPX1]) and peroxisome proliferator activated receptor-γ (PPAR-γ) genotyping results, and stratified based on DM...
December 7, 2016: Nephrology
https://www.readbyqxmd.com/read/27925173/potential-of-long-non-coding-rnas-in-cancer-patients-from-bio-markers-to-therapeutic-targets
#5
REVIEW
Subash Chandra Gupta, Yashoda Nandan Tripathi
Because of high specificity and easy detection in the tissues, serum, plasma, urine and saliva, interest in exploring the potential of long non-coding RNAs (lncRNAs) in cancer patients continues to increase. LncRNAs have shown potential as a bio-marker in the diagnosis and prognosis of bladder cancer, prostate cancer, gastric cancer, pancreatic cancer, breast cancer, and many other cancer types. Some lncRNAs have also been used as adjunct to improve the specificity and sensitivity of existing biomarkers. The molecular tools such as RNA-seq, RNA-FISH, ic-SHAPE and quantitative real-time PCR have been used for examining the lncRNAs' potential...
December 7, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27925170/associations-of-microrna-single-nucleotide-polymorphisms-and-disease-risk-and-pathophysiology
#6
REVIEW
Xiaoxiao Liu, Zhijun Han, Chengjian Yang
Single nucleotide polymorphisms (SNPs) are genetic variations that contribute to human phenotypes associated with various diseases. SNPs are involved in the regulation of a broad range of physiological and pathological processes, such as cellular senescence, apoptosis, inflammation, and immune response, by up-regulating the expression of classical inflammation markers. Recent studies have suggested that SNPs located in gene-encoding microRNAs (miRNAs) affect various aspects of diseases by regulating the expression or activity of miRNAs...
December 7, 2016: Clinical Genetics
https://www.readbyqxmd.com/read/27925136/multidimensional-evaluation-of-endogenous-and-health-factors-affecting-food-preferences-taste-and-smell-perception
#7
D Guido, S Perna, M Carrai, R Barale, M Grassi, M Rondanelli
OBJECTIVE: This study, by taking a holistic approach, investigates the relationships between taste, smell sensitivity and food preference with prognostic (endogenous and health) factors including age, gender, genetic taste markers, body mass, cigarette smoking, and number of drugs used. DESIGN: Cross sectional study. SETTING: Northern Italy. PARTICIPANTS: 203 healthy subjects (160 women/43 men; mean age: 58.2±19.8 years) were examined...
2016: Journal of Nutrition, Health & Aging
https://www.readbyqxmd.com/read/27925035/insulin-like-growth-factor-1-gene-polymorphism-and-breast-cancer-risk
#8
Danylo R Costa-Silva, Maria DA Conceição Barros-Oliveira, Rafael S Borges, Cléciton B Tavares, Umbelina S Borges, Francisco A Alves-Ribeiro, Vladimir C Silva, Benedito B DA Silva
Insulin-like Growth Factor-1 (IGF-1) gene polymorphism has been associated with an increased risk for breast cancer. IGF-1 is a key regulator of proliferation, cell differentiation and apoptosis. It has important mitogenic and anti-apoptotic activities in normal cells and in breast cancer cells, acting synergistically with estrogen to increase neoplastic cell proliferation. This review aims to present the recent finds of IGF-1 gene polymorphism and its relationship with the risk of breast cancer through following the polymorphic dinucleotide repeat cytosine-adenine (CA) and single nucleotide polymorphisms (SNPs) by searching in the PubMed database publications focused studies published from 2010 to 2015 related to IGF-1 gene polymorphism and breast cancer risk...
December 1, 2016: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/27924947/two-genomic-regions-associated-with-fiber-quality-traits-in-chinese-upland-cotton-under-apparent-breeding-selection
#9
Junji Su, Libei Li, Chaoyou Pang, Hengling Wei, Caixiang Wang, Meizhen Song, Hantao Wang, Shuqi Zhao, Chi Zhang, Guangzhi Mao, Long Huang, Chengshe Wang, Shuli Fan, Shuxun Yu
Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924921/birth-weight-and-risk-of-ischemic-heart-disease-a-mendelian-randomization-study
#10
Shiu Lun Au Yeung, Shi Lin Lin, Albert Martin Li, C Mary Schooling
Low birth weight is a risk factor for cardiovascular disease. However, the association could be confounded by many factors. We used Mendelian randomization to clarify the role of birth weight in ischemic heart disease (IHD) and lipids. We used all 7 single nucleotide polymorphisms (SNPs) independently contributing to birth weight at genome wide significance (p < 5 × 10(-8)) in separate sample instrumental variable analysis to estimate the effect of birth weight on IHD using the CARDIoGRAMplusC4D 1000 Genomes based GWAS case (n = 60,801)-control (n = 123,504) study and on lipids using GLGC (n = 188,577)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924804/association-of-myh9-polymorphisms-with-hypertension-in-patients-with-chronic-kidney-disease-in-china
#11
Liping Liu, Caili Wang, Yan Mi, Dan Liu, Li Li, Junying Fan, Lei Nan, Niya Jia, Yu Du
BACKGROUND/AIMS: This study explored the correlation between hypertension and non-muscle myosin heavy chain 9 (MYH9) gene polymorphisms in Chinese chronic kidney disease (CKD) patients. METHODS: This case-control study included 301 patients with CKD and 293 healthy controls. The E1 haplotype single nucleotide polymorphisms (SNPs) rs3752462 and rs4821480 were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. The association between MYH9 polymorphisms and high systolic blood pressure (SBP ≥ 140 mmHg) susceptibility in CKD patients was analysed...
December 8, 2016: Kidney & Blood Pressure Research
https://www.readbyqxmd.com/read/27924448/milk-protein-polymorphisms-and-casein-haplotypes-in-butana-cattle
#12
A Said Ahmed, S Rahmatalla, R Bortfeldt, D Arends, M Reissmann, G A Brockmann
Butana is a Bos indicus dairy cattle breed that is well adapted to the local environment of Sudan. The breed has been gradually declining in number due to breed substitution. Therefore, conservation and improvement strategies are required to maintain this breed. The aim of the present study was to assess genetic variation that is characteristic for Butana cattle in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB. In a first step, genomic DNA of five unrelated individuals was comparatively sequenced across all exon and flanking sequences...
December 6, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27924447/associations-between-polymorphisms-in-the-nicd-domain-of-bovine-notch1-gene-and-growth-traits-in-chinese-qinchuan-cattle
#13
Mei Liu, Chenge Zhang, Xinsheng Lai, Jing Xue, Xianyong Lan, Chuzhao Lei, Yutang Jia, Hong Chen
NOTCH1 is one of the four mammalian Notch receptors, which is involved in the Notch signaling pathway. Specifically, NOTCH1 promotes the proliferation of myogenic precursor cells, and the NICD domain of NOTCH1 can impair regeneration of skeletal muscles. However, similar research on the bovine NOTCH1 gene is lacking. In this study, we detected the polymorphisms of the bovine NOTCH1 gene in a total of 448 individuals from Chinese Qinchuan cattle with DNA pooling, forced PCR-RFLP, and DNA sequencing methods. Five novel SNPs were identified within the NICD domain, and eight haplotypes comprising combinations of these five SNPs were studied as well...
December 6, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27924156/deficiency-of-atp6v1h-causes-bone-loss-by-inhibiting-bone-resorption-and-bone-formation-through-the-tgf-%C3%AE-1-pathway
#14
Xiaohong Duan, Jin Liu, Xueni Zheng, Zhe Wang, Yanli Zhang, Ying Hao, Tielin Yang, Hongwen Deng
Vacuolar-type H (+)-ATPase (V-ATPase) is a highly conserved, ancient enzyme that couples the energy of ATP hydrolysis to proton transport across vesicular and plasma membranes of eukaryotic cells. Previously reported mutations of various V-ATPase subunits are associated with increased bone density. We now show that haploinsufficiency for the H subunit of the V1 domain (ATP6V1H) is associated with osteoporosis in humans and mice. A genome-wide SNP array analysis of 1625 Han Chinese found that 4 of 15 tag SNPs (26...
2016: Theranostics
https://www.readbyqxmd.com/read/27924034/comprehensive-characterization-annotation-and-innovative-use-of-infinium-dna-methylation-beadchip-probes
#15
Wanding Zhou, Peter W Laird, Hui Shen
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3' nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27924020/lincsnp-2-0-an-updated-database-for-linking-disease-associated-snps-to-human-long-non-coding-rnas-and-their-tfbss
#16
Shangwei Ning, Ming Yue, Peng Wang, Yue Liu, Hui Zhi, Yan Zhang, Jizhou Zhang, Yue Gao, Maoni Guo, Dianshuang Zhou, Xin Li, Xia Li
We describe LincSNP 2.0 (http://bioinfo.hrbmu.edu.cn/LincSNP), an updated database that is used specifically to store and annotate disease-associated single nucleotide polymorphisms (SNPs) in human long non-coding RNAs (lncRNAs) and their transcription factor binding sites (TFBSs). In LincSNP 2.0, we have updated the database with more data and several new features, including (i) expanding disease-associated SNPs in human lncRNAs; (ii) identifying disease-associated SNPs in lncRNA TFBSs; (iii) updating LD-SNPs from the 1000 Genomes Project; and (iv) collecting more experimentally supported SNP-lncRNA-disease associations...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923803/whole-exome-sequencing-validates-a-preclinical-mouse-model-for-the-prevention-and-treatment-of-cutaneous-squamous-cell-carcinoma
#17
Elena V Knatko, Brandon Praslicka, Maureen Higgins, Alan Evans, Karin J Purdie, Catherine A Harwood, Charlotte M Proby, Aikseng Ooi, Albena T Dinkova-Kostova
Cutaneous squamous cell carcinomas (cSCC) are among the most common and highly mutated human malignancies. Solar UV radiation is the major factor in the etiology of cSCC. Whole exome sequencing of 18 microdissected tumor samples (cases) derived from SKH-1 hairless mice that had been chronically exposed to solar-simulated UV (SSUV) radiation showed a median point mutation (single nucleotide polymorphism, SNP) rate of 155 per megabase. The majority (78.6%) of the SNPs are C.G>T.A transitions, a characteristic UVR-induced mutational signature...
December 6, 2016: Cancer Prevention Research
https://www.readbyqxmd.com/read/27923663/pharmacogenetics-of-lithium-effects-on-glomerular-function-in-bipolar-disorder-patients-under-chronic-lithium-treatment-a-pilot-study
#18
Evangelia Eirini Tsermpini, Yanfei Zhang, Paola Niola, Caterina Chillotti, Raffaella Ardau, Alberto Bocchetta, George P Patrinos, Maria Del Zompo, Giovanni Severino, Ming Ta Michael Lee, Alessio Squassina
Bipolar disorder (BD) is a psychiatric disease characterized by alternating episodes of mania and depression. Lithium (Li) represents the mainstay treatment for BD, although a significant proportion of patients show insufficient or no response. Li is also associated with potentially severe side effects, including renal effects. Several studies reported that Li may induce reduction of glomerular filtration rate (GFR) in patients under long-term treatment. The biological systems and the genetic factors involved in susceptibility to Li-induced renal-side effects have been scarcely explored...
December 3, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27923415/association-of-body-mass-index-related-single-nucleotide-polymorphisms-with-psychiatric-disease-and-memory-performance-in-a-japanese-population
#19
Midori Ninomiya-Baba, Junko Matsuo, Daimei Sasayama, Hiroaki Hori, Toshiya Teraishi, Miho Ota, Kotaro Hattori, Takamasa Noda, Ikki Ishida, Shigenobu Shibata, Hiroshi Kunugi
OBJECTIVE: Obesity is a risk factor for psychiatric diseases. Recently, a number of single nucleotide polymorphisms (SNPs) have been shown to be related to body mass index (BMI). In this study, we investigated the association of BMI-related SNPs with psychiatric diseases and one of their endophenotypes, memory performance, in a Japanese population. METHODS: The subjects were 1624 patients with one of three psychiatric diseases (799 patients with major depressive disorder, 594 with schizophrenia, and 231 with bipolar disorder) and 1189 healthy controls...
December 7, 2016: Acta Neuropsychiatrica
https://www.readbyqxmd.com/read/27923400/allele-specific-expression-in-the-human-heart-and-its-application-to-postoperative-atrial-fibrillation-and-myocardial-ischemia
#20
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jon G Seidman, Simon C Body, Jochen D Muehlschlegel
BACKGROUND: Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE to identify genes associated with postoperative atrial fibrillation (poAF) and myocardial ischemia. METHODS: Following genotyping from whole blood and whole-genome sequencing of LA and LV samples, we called ASE using sequences overlapping heterozygous SNPs using rigorous quality control to minimize false ASE calling...
December 6, 2016: Genome Medicine
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