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https://www.readbyqxmd.com/read/28938720/deep-whole-genome-sequencing-of-90-han-chinese-genomes
#1
Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mengcheng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938719/population-wide-sampling-of-retrotransposon-insertion-polymorphisms-using-deep-sequencing-and-efficient-detection
#2
Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lu, Xiaosen Guo, Guibo Li, Yong Hou, Shiping Liu, Bo Li
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938685/a-case-control-study-of-the-association-between-the-egfr-gene-and-glioma-risk-in-a-chinese-han-population
#3
Mengdan Yan, Jingjie Li, Na He, Xugang Shi, Shuli Du, Bin Li, Tianbo Jin
The Epidermal Growth Factor Receptor gene has been reported to be involved in the progression of gliomas which is one of the deadliest primary brain tumors in humans. To determine potential association between EGFR and glioma risk, we performed a case-control study with 394 glioma patients and 298 cancer-free controls in which captured a total of 8 tag single nucleotide polymorphisms of EGFR gene from Xi'an, China. SPSS 19.0 statistical packages, χ(2) test, genetic model analysis and SHEsis software platform were analyzed s the variants in EGFR gene associations with glioma risk...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938673/quantitative-assessment-of-lncrna-hotair-polymorphisms-and-cancer-risk-in-chinese-population-a-meta-analysis-based-on-26-810-subjects
#4
Xu Liu, Qiongyu Duan, Jian Zhang
As a well-known long non-coding RNA, HOTAIR has been demonstrated to be involved in carcinogenesis and progression of various human cancers. Previous studies have investigated the potential association between HOTAIR polymorphisms and cancer risk in Chinese population. However, the results remain conflicting. Therefore, for the first time, we conducted a meta-analysis to derive a more precise estimation of these associations for Chinese. PubMed, Embase, CNKI and Wanfang databases were systematically searched...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938665/meta-analysis-of-the-association-of-the-cyp2j2-g-50t-polymorphism-with-coronary-artery-disease
#5
Jian Chen, Dong-Fei Wang, Guo-Dong Fu, Jie Ding, Lei-Yang Chen, Jia-Lan Lv, Juan Fang, Xiang Yin, Xiao-Gang Guo
The association of the CYP2J2 G-50T polymorphism with coronary artery disease has been explored, but the results remain controversial. Thus, a meta-analysis was conducted to provide a comprehensive estimate of this association. We selected ten articles encompassing 12 independent case-control studies with 7063 cases and 10,453 controls for this meta-analysis. Overall, we found significant associations between the CYP2J2 G-50T polymorphism and coronary artery disease risk in three genetic models (allele model: odds ratio (OR) = 1...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938654/methylenetetrahydrofolate-reductase-c677t-polymorphism-and-the-risks-of-polycystic-ovary-syndrome-an-updated-meta-analysis-of-14-studies
#6
Lihong Wang, Wenting Xu, Caihong Wang, Mengyu Tang, Yujia Zhou
Some studies have reported an association between the Methylenetetrahydrofolate reductase (MTHFR) C667T genetic variant and risk of polycystic ovary syndrome (PCOS), although the results remain controversial. A systematic search was conducted on PubMed, Web of Science, EMBASE, Ovid, Chinese National Knowledge Databases and WanFang databases with relevant keywords. Fourteen studies of sixteen distinct populations involving 1478 PCOS cases and used to conduct a meta-analysis. The T allele was not significantly associated with increased risk of PCOS [OR: 1...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938645/sex-specific-association-of-sh2b3-and-smarca4-polymorphisms-with-coronary-artery-disease-susceptibility
#7
Yuqiang Ji, Yanbin Song, Qingwen Wang, Pengcheng Xu, Zhao Zhao, Xia Li, Nan Wang, Tianbo Jin, Chao Chen
To determine whether sex differences affect the association between genetic polymorphisms and coronary artery disease (CAD) in the Chinese Han population, we conducted a study comparing the frequency of SH2B3 and SMARCA4 variants in 456 CAD patients (291 men, 165 women) and 685 age-matched controls (385 men, 300 women). Ten single nucleotide polymorphisms (SNPs) in SH2B3 and SMARCA4 were genotyped using MassARRAY technology. Allelic and genotypic models and haplotype frequencies were compared between groups...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938640/association-of-two-obesity-related-gene-polymorphisms-lepg2548a-rs7799039-and-leprq223r-rs1137101-with-the-risk-of-breast-cancer
#8
Hui Luan, Hong Zhang, Ying Li, Ping Wang, Lifei Cao, Honglan Ma, Qing Cui, Gang Tian
Many studies have been performed to investigate the correlation of leptin (LEP) and leptin receptor (LEPR) polymorphisms with breast cancer (BC) risk, however the results are inconclusive. To obtain a more precise estimation, we conducted this meta-analysis. We searched PubMed, EMBASE, and Web of Science databases to identify qualified studies. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate the association. Eight eligible studies (2,124 cases and 5,476 controls) for LEP G2548A (rs7799039) polymorphism, and thirteen studies (5,282 cases and 6,140 controls) for LEPR Q223R (rs1137101) polymorphism were included in our study...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938476/fetal-and-maternal-genetic-variants-influencing-neonatal-vitamin-d-status
#9
Ketil Størdal, Karl Mårild, German Tapia, Margareta Haugen, Arieh S Cohen, Benedicte A Lie, Lars C Stene
Objective: Several genetic polymorphisms determine vitamin D status. We aimed to estimate the strength of association of established 25-hydroyxvitamin D (25OHD) associated variants in the mother and in the fetus, with 25OHD concentration in newborn umbilical cord plasma. Methods: We randomly selected 578 mother and child dyads from the prospective Norwegian Mother and Child Cohort study (MoBa). 25OHD was assayed in maternal samples taken shortly after delivery and in cord samples...
August 18, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28938457/the-association-of-estrogen-receptor-%C3%AE-gene-variation-with-salt-sensitive-blood-pressure
#10
Worapaka Manosroi, Jia Wei Tan, Chevon M Rariy, Bei Sun, Mark O Goodarzi, Aditi R Saxena, Jonathan S Williams, Luminita H Pojoga, Jessica Lasky-Su, Jinrui Cui, Xiuqing Guo, Kent D Taylor, Yii-Der I Chen, Anny H Xiang, Willa A Hsueh, Leslie J Raffel, Thomas A Buchanan, Jerome I Rotter, Gordon H Williams, Ellen W Seely
Context: Hypertension in young women is uncommon compared to young men and older women. Estrogen appears to protect most women against hypertension with incidence increasing after menopause. Since some premenopausal women develop hypertension, estrogen may play a different role in these women. Genetic variations in the estrogen receptor (ER) are associated with cardiovascular disease. ER-β, encoded by ESR2, is the ER predominantly expressed in vascular smooth muscle. Objective: To determine an association of single nucleotide polymorphisms (SNPs) in ESR2 with salt-sensitivity of blood pressure (SSBP) and estrogen status in women...
September 5, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28938222/inter-hemispherical-asymmetry-in-default-mode-functional-connectivity-and-baiap2-gene-are-associated-with-anger-expression-in-adhd-adults
#11
R Hasler, M G Preti, D E Meskaldji, J Prados, W Adouan, C Rodriguez, S Toma, N Hiller, T Ismaili, J Hofmeister, I Sinanaj, P Baud, S Haller, P Giannakopoulos, S Schwartz, N Perroud, D Van De Ville
Attention deficit hyperactivity disorder (ADHD) is accompanied by resting-state alterations, including abnormal activity, connectivity and asymmetry of the default-mode network (DMN). Concurrently, recent studies suggested a link between ADHD and the presence of polymorphisms within the gene BAIAP2 (i.e., brain-specific angiogenesis inhibitor 1-associated protein 2), known to be differentially expressed in brain hemispheres. The clinical and neuroimaging correlates of this polymorphism are still unknown. We investigated the association between BAIAP2 polymorphisms and DMN functional connectivity (FC) asymmetry as well as behavioral measures in ADHD adults...
September 12, 2017: Psychiatry Research
https://www.readbyqxmd.com/read/28938149/the-genetic-influence-in-fluorosis
#12
REVIEW
Sreemanta Pramanik, Depanwita Saha
Fluorosis, caused by ingestion of excess fluoride, is endemic in at least 25 countries across the globe, China and India being the worst affected among them. Dental, skeletal and non-skeletal are the major types of fluorosis affecting millions of people in these countries. A number of genetic epidemiological studies carried out by investigators have shown the evidence for association between genetic polymorphisms in candidate genes and differences in the susceptibility pattern of different types of fluorosis among individuals living in the same community and having the same environmental exposure...
September 15, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28938133/genetic-polymorphisms-for-19-x-str-loci-of-sichuan-han-ethnicity-and-its-comparison-with-chinese-populations
#13
Guanglin He, Ye Li, Xing Zou, Mengge Wang, Pengyu Chen, Miao Liao, Jin Wu
X-chromosomal short tandem repeats (X-STRs) can be serviced as a complementary tool in forensic deficiency cases and other complicated kinship identification. To investigate the genetic variation of the western Chinese Han population, genetic polymorphisms of 19 X-STR loci (DXS8378, DXS7423, DXS10148, DXS10159, DXS10134, DXS7424, DXS10164, DXS10162, DXS7132, DXS10079, DXS6789, DXS101, DXS10103, DXS10101, HPRTB, DXS6809, DXS10075, DXS10074 and DXS10135) included in the AGCU X19 PCR amplification kit were obtained from 201 Chinese Han individuals (108 females and 93 males) residing in Sichuan province, western China...
September 15, 2017: Legal Medicine
https://www.readbyqxmd.com/read/28937897/the-role-of-genetic-factors-in-the-outbreak-mechanism-of-dental-caries
#14
Junko Shimomura-Kuroki, Tomoko Nashida, Yukio Miyagawa, Tsuneo Sekimoto
OBJECTIVE: The aim of the present study was to investigate the relationships between cariogenic bacterial infection and single nucleotide polymorphisms (SNPs) in candidate genes associated with dental caries, and to explore the factors related to caries in children. STUDY DESIGN: Children aged 3 to 11 years were selected. Detection of cariogenic bacteria (Streptococcus mutans, Streptococcus oralis, Streptococcus sobrinus and Lactobacillus) from the plaque of each patient, and SNP analyses of five candidate genes (MBL2, TAS2R38, GLUT2, MMP13 and CA6) were performed using DNA isolated from buccal mucosal cells...
September 22, 2017: Journal of Clinical Pediatric Dentistry
https://www.readbyqxmd.com/read/28937812/predator-perspective-drives-geographic-variation-in-frequency-dependent-polymorphism
#15
Iris A Holmes, Maggie R Grundler, Alison R Davis Rabosky
Color polymorphism in natural populations can manifest as a striking patchwork of phenotypes in space, with neighboring populations characterized by dramatic differences in morph composition. These geographic mosaics can be challenging to explain in the absence of localized selection because they are unlikely to result from simple isolation-by-distance or clinal variation in selective regimes. To identify processes that can lead to the formation of geographic mosaics, we developed a simulation-based model to explore the influence of predator perspective, selection, migration, and genetic linkage of color loci on allele frequencies in polymorphic populations over space and time...
October 2017: American Naturalist
https://www.readbyqxmd.com/read/28937693/genome-wide-association-study-of-alcohol-consumption-and-genetic-overlap-with-other-health-related-traits-in-uk-biobank-n-112%C3%A2-117
#16
T-K Clarke, M J Adams, G Davies, D M Howard, L S Hall, S Padmanabhan, A D Murray, B H Smith, A Campbell, C Hayward, D J Porteous, I J Deary, A M McIntosh
Alcohol consumption has been linked to over 200 diseases and is responsible for over 5% of the global disease burden. Well-known genetic variants in alcohol metabolizing genes, for example, ALDH2 and ADH1B, are strongly associated with alcohol consumption but have limited impact in European populations where they are found at low frequency. We performed a genome-wide association study (GWAS) of self-reported alcohol consumption in 112 117 individuals in the UK Biobank (UKB) sample of white British individuals...
October 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28937232/physiology-of-nitric-oxide-in-the-respiratory-system
#17
M Antosova, D Mokra, L Pepucha, J Plevkova, T Buday, M Sterusky, A Bencova
Nitric oxide (NO) is an important endogenous neurotransmitter and mediator. It participates in regulation of physiological processes in different organ systems including airways. Therefore, it is important to clarify its role in the regulation of both airway and vascular smooth muscle, neurotransmission and neurotoxicity, mucus transport, lung development and in the. surfactant production. The bioactivity of NO is highly variable and depends on many factors: the presence and activity of NO-producing enzymes, activity of competitive enzymes (e...
September 22, 2017: Physiological Research
https://www.readbyqxmd.com/read/28937055/association-between-apolipoprotein-e-polymorphism-and-nephropathy-in-iranian-diabetic-patients
#18
Mostafa Karimoei, Parvin Pasalar, Mohsen Mehrabzadeh, Maryam Daneshpour, Maryam Shojaee, Katayoun Forouzanfar, Farideh Razi
Approximately one-third of diabetic patients develop evidence of nephropathy. Pathogenesis of diabetic nephropathy (DN) remains unclear; however, some genetic and metabolic risk factors have been determined for the development and progression of DN. In the recent genetic studies, polymorphism of apolipoprotein E (ApoE) gene has been reported as a risk factor for the development of DN; however, the results are inconsistent. The aim of the present study was to evaluate the association between ApoE polymorphism and nephropathy in Iranian patient with type 2 diabetes...
September 2017: Saudi Journal of Kidney Diseases and Transplantation
https://www.readbyqxmd.com/read/28936983/teaching-practice-and-experiences-of-verifying-the-three-laws-of-genetics-based-on-the-sslp-marker-analysis
#19
Xue-Ying Huang, Kai Fan, Yan-Fang Ye, Bin Wang, Wei-Ren Wu, Tao Lan
We explored the practical effect of the genetic analysis of simple sequence length polymorphism (SSLP) molecular markers in rice in the genetics lab course. Two parents and their F2 population were analyzed and detected with three SSLP molecular markers that located on two chromosomes of the rice genome. The markers' genotype data were used to verify the three laws of genetics, including segregation, independent assortment and linkage and crossing-over. Our practice has proved not only beneficial to deepen students' understandings about the three laws of genetics, but also conducive to cultivate students' interests in research and innovation and improve their skills and comprehensive analysis abilities...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28936945/sources-of-fungal-genetic-variation-and-associating-it-with-phenotypic-diversity
#20
John W Taylor, Sara Branco, Cheng Gao, Chris Hann-Soden, Liliam Montoya, Iman Sylvain, Pierre Gladieux
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability...
September 2017: Microbiology Spectrum
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