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https://www.readbyqxmd.com/read/28637339/emergence-of-ceftazidime-avibactam-non-susceptibility-in-an-mdr-klebsiella-pneumoniae-isolate
#1
Anna Both, Henning Büttner, Jiabin Huang, Markus Perbandt, Cristina Belmar Campos, Martin Christner, Florian P Maurer, Stefan Kluge, Christina König, Martin Aepfelbacher, Dominic Wichmann, Holger Rohde
Background: Avibactam is a novel broad-range β-lactamase inhibitor active against Ambler class A (including ESBL and KPC) and some Ambler class C and D (e.g. OXA-48) enzymes. We here report on the emergence of ceftazidime/avibactam resistance in clinical, multiresistant, OXA-48 and CTX-M-14-producing Klebsiella pneumoniae isolate DT12 during ceftazidime/avibactam treatment. Methods and results: Comparative whole-genome sequence analysis identified two SNPs in the CTX-M-14-encoding gene leading to two amino acid changes (P170S and T264I)...
June 16, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28637279/high-dimensional-multivariate-mediation-with-application-to-neuroimaging-data
#2
Oliver Y Chén, Ciprian Crainiceanu, Elizabeth L Ogburn, Brian S Caffo, Tor D Wager, Martin A Lindquist
Mediation analysis is an important tool in the behavioral sciences for investigating the role of intermediate variables that lie in the path between a treatment and an outcome variable. The influence of the intermediate variable on the outcome is often explored using a linear structural equation model (LSEM), with model coefficients interpreted as possible effects. While there has been significant research on the topic, little work has been done when the intermediate variable (mediator) is a high-dimensional vector...
June 15, 2017: Biostatistics
https://www.readbyqxmd.com/read/28637275/16gt-a-fast-and-sensitive-variant-caller-using-a-16-genotype-probabilistic-model
#3
Ruibang Luo, Michael C Schatz, Steven L Salzberg
16GT is a variant caller for Illumina whole-genome and whole-exome sequencing data. It uses a new 16-genotype probabilistic model to unify SNP and indel calling in a single variant calling algorithm. In benchmark comparisons with five other widely used variant callers on a modern 36-core server, 16GT demonstrated improved sensitivity in calling SNPs, and it provided comparable sensitivity and accuracy for calling indels as compared to the GATK HaplotypeCaller. 16GT is available at https://github.com/aquaskyline/16GT...
June 15, 2017: GigaScience
https://www.readbyqxmd.com/read/28637217/experimental-support-that-natural-selection-has-shaped-the-latitudinal-distribution-of-mitochondrial-haplotypes-in-australian-drosophila-melanogaster
#4
M Florencia Camus, Jonci N Wolff, Carla M Sgrò, Damian K Dowling
Cellular metabolism is regulated by enzyme complexes within the mitochondrion, the function of which are sensitive to the prevailing temperature. Such thermal sensitivity, coupled with the observation that population frequencies of mitochondrial haplotypes tend to associate with latitude, altitude or climatic regions across species distributions, led to the hypothesis that thermal selection has played a role in shaping standing variation in the mitochondrial DNA (mtDNA) sequence. This hypothesis, however, remains controversial, and requires evidence that the distribution of haplotypes observed in nature corresponds with the capacity of these haplotypes to confer differences in thermal tolerance...
June 20, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28636766/association-of-tnfsf13-polymorphisms-with-iga-nephropathy-in-chinese-han-population
#5
Zhong Zhong, Shao-Zhen Feng, Ri-Cong Xu, Zhi-Jian Li, Feng-Xian Huang, Pei-Ran Yin, Wen-Ting Liu, Meng Wang, Dian-Chun Shi, Qian Zhou, Xue-Qing Yu, Ming Li
BACKGROUND: Our previous genome-wide association study (GWAS) of IgA nephropathy (IgAN) in Chinese Han population suggested that TNFSF13 gene may be a novel susceptibility gene for IgAN. In this study, we aim to further evaluate the associations of single-nucleotide polymorphisms (SNPs) and expression level of TNFSF13 gene with the risk and clinical parameters of IgAN. METHODS: Six candidate SNPs were selected for genotyping by Sequenom MassARRAY iPLEX in 1000 IgAN cases and 1000 controls...
June 21, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28636552/meta-analysis-of-the-association-between-three-microrna-polymorphisms-and-breast-cancer-susceptibility
#6
Kun Mu, Zi-Zheng Wu, Jin-Pu Yu, Wei Guo, Nan Wu, Li-Juan Wei, Huan Zhang, Jing Zhao, Jun-Tian Liu
Single nucleotide polymorphisms (SNPs) in three microRNAs (miRNAs), rs2910164 in miR-146a, rs11614913 in miR-196a2, and rs3746444 in miR-499, have been associated with breast cancer (BC) susceptibility, but the evidence is conflicting. To obtain a more robust assessment of the association between these miRNA variants and BC risk, we carried out a meta-analysis through systematic literature retrieval from the PubMed and Embase databases. A total of 9 case-control studies on rs2910164, 12 on rs11614913, and 7 on rs3746444 were included...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636460/evaluation-of-bovine-high-density-snp-genotyping-array-in-indigenous-dairy-cattle-breeds
#7
S Dash, A Singh, A K Bhatia, S Jayakumar, A Sharma, S Singh, I Ganguly, S P Dixit
In total 52 samples of Sahiwal ( 19 ), Tharparkar ( 17 ), and Gir ( 16 ) were genotyped by using BovineHD SNP chip to analyze minor allele frequency (MAF), genetic diversity, and linkage disequilibrium among these cattle. The common SNPs of BovineHD and 54K SNP Chips were also extracted and evaluated for their performance. Only 40%-50% SNPs of these arrays was found informative for genetic analysis in these cattle breeds. The overall mean of MAF for SNPs of BovineHD SNPChip was 0.248 ± 0.006, 0.241 ± 0...
June 21, 2017: Animal Biotechnology
https://www.readbyqxmd.com/read/28636232/a-genetic-stochastic-process-model-for-genome-wide-joint-analysis-of-biomarker-dynamics-and-disease-susceptibility-with-longitudinal-data
#8
Liang He, Ilya Zhbannikov, Konstantin G Arbeev, Anatoliy I Yashin, Alexander M Kulminski
Unraveling the underlying biological mechanisms or pathways behind the effects of genetic variations on complex diseases remains one of the major challenges in the post-GWAS (where GWAS is genome-wide association study) era. To further explore the relationship between genetic variations, biomarkers, and diseases for elucidating underlying pathological mechanism, a huge effort has been placed on examining pleiotropic and gene-environmental interaction effects. We propose a novel genetic stochastic process model (GSPM) that can be applied to GWAS and jointly investigate the genetic effects on longitudinally measured biomarkers and risks of diseases...
June 21, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#9
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635422/metallothionein-polymorphisms-in-a-northern-spanish-population-with-neovascular-and-dry-forms-of-age-related-macular-degeneration
#10
Montserrat García, Lydia Álvarez, Ángela Fernández, Héctor González-Iglesias, Julio Escribano, Beatriz Fernández-Vega, Eva Villota, Luis Fernández-Vega Cueto, Álvaro Fernández-Vega, Miguel Coca-Prados
BACKGROUND: To elucidate the potential role of single nucleotide polymorphisms (SNPs) in the metallothionein (MT) genes in Northern Spanish patients with age-related macular degeneration (AMD). METHODS: A total of 130 unrelated Northern Spanish natives diagnosed with AMD (46 dry, 35 neovascular, and 49 mixed) and 96 healthy controls, matched by age and ethnicity, were enrolled in a case-control study. DNA was isolated from peripheral blood and genotyped for 14 SNPs located at 5 MT genes (MT1A: rs11076161, rs 11640851, rs8052394, and rs7196890; MT1B: rs8052334, rs964372, and rs7191779; MT1M: rs2270836 and rs9936741; MT2A: rs28366003, rs1610216, rs10636, and rs1580833; MT3: rs45570941) using TaqMan probes...
March 1, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28635360/the-association-between-apolipoprotein-a1-c3-a5-gene-cluster-promoter-polymorphisms-and-risk-of-ischemic-stroke-in-the-northern-chinese-han-population
#11
Yanzhe Wang, Fang Liu, Lei Li, Shumin Deng, Zhiyi He
Objective Given its effects on lipid metabolism, the apolipoprotein A1-C3-A5 ( APOA1-C3-A5) gene cluster is thought to play an important role in ischemic stroke pathogenesis. Here, we evaluated whether the APOA1-C3-A5 cluster is associated with ischemic stroke in the northern Chinese Han population. Methods This case-control study analyzed 812 patients with ischemic stroke and 844 healthy controls with regard to four APOA1-C3-A5 cluster promoter single nucleotide polymorphisms (SNPs), rs670, rs2854116, rs2854117, and rs662799, using the SNaPshot Multiplex sequencing assay...
January 1, 2017: Journal of International Medical Research
https://www.readbyqxmd.com/read/28634826/tai-vacuolar-invertase-orthologs-the-interspecific-variability-in-tomato-plants-solanum-section-lycopersicon
#12
M A Slugina, A V Shchennikova, E Z Kochieva
Understanding the genetic mechanisms underlying carbohydrate metabolism can promote the development of biotechnological advances in fruit plants. The flesh tomato fruit represents an ideal system for examining the role of sucrose cleavage enzymes in fruit development, and wild tomato species differing in storage sugars serve as an excellent research material for this purpose. Plant vacuolar invertase is a key enzyme of sucrose metabolism in the sink organs. In the present study, we identified complete gene sequences encoding the TAI vacuolar invertase in 11 wild and one cultivated tomato accessions of the Solanum section Lycopersicon...
June 20, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28634715/regulatory-element-based-prediction-identifies-new-susceptibility-regulatory-variants-for-osteoporosis
#13
Shi Yao, Yan Guo, Shan-Shan Dong, Ruo-Han Hao, Xiao-Feng Chen, Yi-Xiao Chen, Jia-Bin Chen, Qing Tian, Hong-Wen Deng, Tie-Lin Yang
Despite genome-wide association studies (GWASs) have identified many susceptibility genes for osteoporosis, it still leaves a large part of missing heritability to be discovered. Integrating regulatory information and GWASs could offer new insights into the biological link between the susceptibility SNPs and osteoporosis. We generated five machine learning classifiers with osteoporosis-associated variants and regulatory features data. We gained the optimal classifier and predicted genome-wide SNPs to discover susceptibility regulatory variants...
June 20, 2017: Human Genetics
https://www.readbyqxmd.com/read/28633642/prediction-and-analysis-of-three-gene-families-related-to-leaf-rust-puccinia-triticina-resistance-in-wheat-triticum-aestivum-l
#14
Fred Y Peng, Rong-Cai Yang
BACKGROUND: The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens...
June 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28633446/genetic-indicators-of-drug-resistance-in-the-highly-repetitive-genome-of-trichomonas-vaginalis
#15
Martina Bradic, Sally D Warring, Grace E Tooley, Paul Scheid, William E Secor, Kirkwood M Land, Po-Jung Huang, Ting-Wen Chen, Chi-Ching Lee, Petrus Tang, Steven A Sullivan, Jane M Carlton
Trichomonas vaginalis, the most common non-viral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633070/length-and-repeat-sequence-variation-in-58-strs-and-94-snps-in-two-spanish-populations
#16
Ferran Casals, Roger Anglada, Núria Bonet, Raquel Rasal, Kristiaan J van der Gaag, Jerry Hoogenboom, Neus Solé-Morata, David Comas, Francesc Calafell
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in 88 Spanish Roma (Gypsy) samples and 143 Catalans. Since this platform is based in massive parallel sequencing, we have used simple R scripts to uncover the sequence variation in the repeat region. Thus, we have found, across 58 STRs, 541 length-based alleles, which, after considering repeat-sequence variation, became 804 different alleles. All loci in both populations were in Hardy-Weinberg equilibrium...
June 16, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28632032/plasminogen-activator-inhibitor-type-1-tag-single-nucleotide-polymorphisms-in-patients-with-diabetes-mellitus-type-2-and-diabetic-retinopathy
#17
Vasileios Siokas, Efthimios Dardiotis, Thomas Sokolakis, Maria Kotoula, Sophia V Tachmitzi, Dimitrios Z Chatzoulis, Pavlina Almpanidou, Ioannis Stefanidis, Georgios M Hadjigeorgiou, Evangelia E Tsironi
BACKGROUND: There is accumulating evidence for genetic susceptibility to the development of diabetic retinopathy (DR). The role of plasminogen activator inhibitor-1 (PAI-1) in DR risk remains controversial. OBJECTIVE: The present study was designed to investigate possible influence of PAI-1 gene region polymorphisms on the risk of DR and on the risk of developing DR early vs late in the course of type 2 diabetes mellitus (T2DM). METHODS: A total of 138 patients with DR, 107 patients with T2DM without DR, and 315 healthy controls were recruited...
February 28, 2017: Current Eye Research
https://www.readbyqxmd.com/read/28631188/role-of-clu-picalm-and-tnk1-genotypes-in-aging-with-and-without-alzheimer-s-disease
#18
Davide Seripa, Francesco Panza, Giulia Paroni, Grazia D'Onofrio, Paola Bisceglia, Carolina Gravina, Maria Urbano, Madia Lozupone, Vincenzo Solfrizzi, Alessandra Bizzarro, Virginia Boccardi, Chiara Piccininni, Antonio Daniele, Giancarlo Logroscino, Patrizia Mecocci, Carlo Masullo, Antonio Greco
Healthy and impaired cognitive aging may be associated to different prevalences of single-nucleotide polymorphisms (SNPs). In a multicenter case-control association study, we studied the SNPs rs11136000 (clusterin, CLU), rs541458 (phosphatidylinositol binding clatrin assembly protein, PICALM), and rs1554948 (transcription factor A, and tyrosine kinase, non-receptor, 1, TNK1) according to the three age groups 50-65 years (group 1), 66-80 years (group 2), and 80+ years (group 3) in 569 older subjects without cognitive impairment (NoCI) and 520 Alzheimer's disease (AD) patients...
June 19, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28630657/arlts1-polymorphism-is-associated-with-an-increased-risk-of-familial-cancer-evidence-from-a-meta-analysis
#19
REVIEW
Yan Jiang, Chen-Yang Zhao, Li-Chun Cheng, Bing Xu, Hui-Yi Lv
Adenosine diphosphate (ADP)-ribosylation factor-like tumour suppressor gene 1(ARLTS1) might be associated with an increased risk of several types of familial cancers. However, previous studies have shown that cancer susceptibility is not completely consistent with ARLTS1 polymorphisms, and the precise mechanism remains unknown. Therefore, we conducted a meta-analysis of case-control studies by searching the PubMed, Embase, OVID, Science Direct and Chinese National Knowledge Infrastructure (CNKI) databases. In total, 12 studies met the inclusion criteria and were included in this meta-analysis...
2017: Hereditary Cancer in Clinical Practice
https://www.readbyqxmd.com/read/28630421/a-genome-wide-association-study-of-anorexia-nervosa-suggests-a-risk-locus-implicated-in-dysregulated-leptin-signaling
#20
Dong Li, Xiao Chang, John J Connolly, Lifeng Tian, Yichuan Liu, Elizabeth J Bhoj, Nora Robinson, Debra Abrams, Yun R Li, Jonathan P Bradfield, Cecilia E Kim, Jin Li, Fengxiang Wang, James Snyder, Maria Lemma, Cuiping Hou, Zhi Wei, Yiran Guo, Haijun Qiu, Frank D Mentch, Kelly A Thomas, Rosetta M Chiavacci, Roger Cone, Bingshan Li, Patrick A Sleiman, Hakon Hakonarson
We conducted a genome-wide association study (GWAS) of anorexia nervosa (AN) using a stringently defined phenotype. Analysis of phenotypic variability led to the identification of a specific genetic risk factor that approached genome-wide significance (rs929626 in EBF1 (Early B-Cell Factor 1); P = 2.04 × 10(-7); OR = 0.7; 95% confidence interval (CI) = 0.61-0.8) with independent replication (P = 0.04), suggesting a variant-mediated dysregulation of leptin signaling may play a role in AN...
June 19, 2017: Scientific Reports
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