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https://www.readbyqxmd.com/read/28096484/evolutionary-dynamics-of-pandemic-methicillin-sensitive-staphylococcus-aureus-st398-and-its-international-spread-via-routes-of-human-migration
#1
Anne-Catrin Uhlemann, Paul R McAdam, Sean B Sullivan, Justin R Knox, Hossein Khiabanian, Raul Rabadan, Peter R Davies, J Ross Fitzgerald, Franklin D Lowy
: Methicillin-susceptible Staphylococcus aureus (MSSA) accounts for the majority of S. aureus infections globally, and yet surprisingly little is known about its clonal evolution. We applied comparative whole-genome sequencing (WGS) analyses to epidemiologically and geographically diverse ST398-MSSA, a pandemic lineage affecting both humans and livestock. Bayesian phylogenetic analysis predicted divergence of human-associated ST398-MSSA ~40 years ago. Isolates from Midwestern pigs and veterinarians differed substantially from those in New York City (NYC)...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28095895/genome-wide-snp-analysis-using-2b-rad-sequencing-identifies-the-candidate-genes-putatively-associated-with-resistance-to-ivermectin-in-haemonchus-contortus
#2
Xiaoping Luo, Xiaona Shi, Chunxiu Yuan, Min Ai, Cheng Ge, Min Hu, Xingang Feng, Xiaoye Yang
BACKGROUND: The excessive and uncontrolled use of anthelmintics, e.g. ivermectin (IVM) for the treatment of livestock parasites has led to widespread resistance in gastrointestinal nematodes, such as Haemonchus contortus. There is an urgent need for better management of drug-use in nematode control and development of novel anthelmintics. Discovery and identification of anthelmintic resistance-associate molecules/markers can provide a basis for rational anthelmintics-use and development of novel drugs...
January 17, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28095416/meta-gwas-accuracy-and-power-metagap-calculator-shows-that-hiding-heritability-is-partially-due-to-imperfect-genetic-correlations-across-studies
#3
Ronald de Vlaming, Aysu Okbay, Cornelius A Rietveld, Magnus Johannesson, Patrik K E Magnusson, André G Uitterlinden, Frank J A van Rooij, Albert Hofman, Patrick J F Groenen, A Roy Thurik, Philipp D Koellinger
Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP) calculator (available at www...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28094815/drd2-co-expression-network-and-a-related-polygenic-index-predict-imaging-behavioral-and-clinical-phenotypes-linked-to-schizophrenia
#4
G Pergola, P Di Carlo, E D'Ambrosio, B Gelao, L Fazio, M Papalino, A Monda, G Scozia, B Pietrangelo, M Attrotto, J A Apud, Q Chen, V S Mattay, A Rampino, G Caforio, D R Weinberger, G Blasi, A Bertolino
Genetic risk for schizophrenia (SCZ) is determined by many genetic loci whose compound biological effects are difficult to determine. We hypothesized that co-expression pathways of SCZ risk genes are associated with system-level brain function and clinical phenotypes of SCZ. We examined genetic variants related to the dopamine D2 receptor gene DRD2 co-expression pathway and associated them with working memory (WM) behavior, the related brain activity and treatment response. Using two independent post-mortem prefrontal messenger RNA (mRNA) data sets (total N=249), we identified a DRD2 co-expression pathway enriched for SCZ risk genes...
January 17, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28094792/identification-of-a-nuclear-respiratory-factor-1-recognition-motif-in-the-apolipoprotein-e-variant-apoe4-linked-to-alzheimer-s-disease
#5
Anne Urfer-Buchwalder, Roman Urfer
Alzheimer's disease affects tens of millions of people worldwide and its prevalence continues to rise. It is caused by a combination of a subject's heredity, environment, lifestyle, and medical condition. The most significant genetic risk factor for late onset Alzheimer's disease is a variant of the apolipoprotein E gene, APOE4. Here we show that the single nucleotide polymorphism rs429358 that defines APOE4 is located in a short sequence motif repeated several times within exon 4 of apolipoprotein E, reminiscent of the structure of transcriptional enhancers...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28093084/association-between-dna-mismatch-repair-gene-polymorphisms-and-platinum-based-chemotherapy-toxicity-in-non-small-cell-lung-cancer-patients
#6
Jun-Yan Liu, Chen-Yue Qian, Yuan-Feng Gao, Juan Chen, Hong-Hao Zhou, Ji-Ye Yin
BACKGROUND: Chemotherapy toxicity is a serious problem from which non-small cell lung cancer (NSCLC) patients suffer. The mismatch repair (MMR) system is associated with platinum-based chemotherapy toxicity in NSCLC patients. In this study, we aimed to investigate the relationship between genetic polymorphisms in the MMR pathway and platinum-based chemotherapy toxicity in NSCLC patients. METHODS: A total of 220 Chinese lung cancer patients who received at least two cycles of platinum-based chemotherapy were recruited for this study...
January 16, 2017: Chinese Journal of Cancer
https://www.readbyqxmd.com/read/28093066/predictive-performance-of-genomic-selection-methods-for-carcass-traits-in-hanwoo-beef-cattle-impacts-of-the-genetic-architecture
#7
Hossein Mehrban, Deuk Hwan Lee, Mohammad Hossein Moradi, Chung IlCho, Masoumeh Naserkheil, Noelia Ibáñez-Escriche
BACKGROUND: Hanwoo beef is known for its marbled fat, tenderness, juiciness and characteristic flavor, as well as for its low cholesterol and high omega 3 fatty acid contents. As yet, there has been no comprehensive investigation to estimate genomic selection accuracy for carcass traits in Hanwoo cattle using dense markers. This study aimed at evaluating the accuracy of alternative statistical methods that differed in assumptions about the underlying genetic model for various carcass traits: backfat thickness (BT), carcass weight (CW), eye muscle area (EMA), and marbling score (MS)...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093065/comparison-of-alternative-approaches-to-single-trait-genomic-prediction-using-genotyped-and-non-genotyped-hanwoo-beef-cattle
#8
Joonho Lee, Hao Cheng, Dorian Garrick, Bruce Golden, Jack Dekkers, Kyungdo Park, Deukhwan Lee, Rohan Fernando
BACKGROUND: Genomic predictions from BayesA and BayesB use training data that include animals with both phenotypes and genotypes. Single-step methodologies allow additional information from non-genotyped relatives to be included in the analysis. The single-step genomic best linear unbiased prediction (SSGBLUP) method uses a relationship matrix computed from marker and pedigree information, in which missing genotypes are imputed implicitly. Single-step Bayesian regression (SSBR) extends SSGBLUP to BayesB-like models using explicitly imputed genotypes for non-genotyped individuals...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093063/whole-genome-sequence-based-genomic-prediction-in-laying-chickens-with-different-genomic-relationship-matrices-to-account-for-genetic-architecture
#9
Guiyan Ni, David Cavero, Anna Fangmann, Malena Erbe, Henner Simianer
BACKGROUND: With the availability of next-generation sequencing technologies, genomic prediction based on whole-genome sequencing (WGS) data is now feasible in animal breeding schemes and was expected to lead to higher predictive ability, since such data may contain all genomic variants including causal mutations. Our objective was to compare prediction ability with high-density (HD) array data and WGS data in a commercial brown layer line with genomic best linear unbiased prediction (GBLUP) models using various approaches to weight single nucleotide polymorphisms (SNPs)...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28092323/brain-substrates-of-reward-processing-and-the-%C3%AE-opioid-receptor-a-pathway-into-pain
#10
Frauke Nees, Susanne Becker, Sabina Millenet, Tobias Banaschewski, Luise Poustka, Arun Bokde, Uli Bromberg, Christian Büchel, Patricia J Conrod, Sylvane Desrivières, Vincent Frouin, Jürgen Gallinat, Hugh Garavan, Andreas Heinz, Bernd Ittermann, Jean-Luc Martinot, Dimitri Papadopoulos Orfanos, Tomáš Paus, Michael N Smolka, Henrik Walter, Rob Whelan, Gunter Schumann, Herta Flor
The processing of reward and reinforcement learning seems to be important determinants of pain chronicity. However, reward processing is already altered early in life and if this is related to the development of pain symptoms later on is not known. The aim of this study was first to examine whether behavioural and brain-related indicators of reward processing at the age of 14 to 15 years are significant predictors of pain complaints 2 years later, at 16 to 17 years. Second, we investigated the contribution of genetic variations in the opioidergic system, which is linked to the processing of both, reward and pain, to this prediction...
February 2017: Pain
https://www.readbyqxmd.com/read/28090334/an-experimental-validation-of-genomic-selection-in-octoploid-strawberry
#11
Salvador A Gezan, Luis F Osorio, Sujeet Verma, Vance M Whitaker
The primary goal of genomic selection is to increase genetic gains for complex traits by predicting performance of individuals for which phenotypic data are not available. The objective of this study was to experimentally evaluate the potential of genomic selection in strawberry breeding and to define a strategy for its implementation. Four clonally replicated field trials, two in each of 2 years comprised of a total of 1628 individuals, were established in 2013-2014 and 2014-2015. Five complex yield and fruit quality traits with moderate to low heritability were assessed in each trial...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28089502/an-extended-fatty-liver-index-to-predict-non-alcoholic-fatty-liver-disease
#12
K Kantartzis, I Rettig, H Staiger, J Machann, F Schick, L Scheja, A Gastaldelli, E Bugianesi, A Peter, M B Schulze, A Fritsche, H-U Häring, N Stefan
BACKGROUND: In clinical practice, there is a strong interest in non-invasive markers of non-alcoholic fatty liver disease (NAFLD). Our hypothesis was that the fold-change in plasma triglycerides (TG) during a 2-h oral glucose tolerance test (fold-change TGOGTT) in concert with blood glucose and lipid parameters, and the rs738409 C>G single nucleotide polymorphism (SNP) in PNPLA3 might improve the power of the widely used fatty liver index (FLI) to predict NAFLD. METHODS: The liver fat content of 330 subjects was quantified by (1)H-magnetic resonance spectroscopy...
January 12, 2017: Diabetes & Metabolism
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#13
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087757/alternative-transcription-of-sodium-bicarbonate-transporter-slc4a7-gene-enhanced-by-single-nucleotide-polymorphisms
#14
Hae Jeong Park, Soojung Lee, Eunji Ju, Jayre A Jones, Inyeong Choi
Genome-wide association studies have identified the single nucleotide polymorphism (SNP) rs3278 in the human SLC4A7 gene as one of the marker loci for addiction vulnerability. This marker is located in an intron of the gene, and its genomic role has been unknown. In this study, we examined rs3278 and three adjacent SNPs prevalent in alcoholics for their effects on an alternative promoter that would lead to the production of the N-terminally truncated protein NBCn1ΔN450, missing the first 450 amino acids. Analysis of the transcription start site database and a promoter prediction algorithm identified a cluster of three promoters in intron 7 and two short CpG-rich sites in intron 6...
January 13, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28081591/new-perspectives-of-biomarkers-for-the-management-of-chronic-hepatitis-b
#15
REVIEW
Chih-Lin Lin, Jia-Horng Kao
With recent advances in molecular and genomic investigations, the impact of hepatitis B viral and host factors on the progression of chronic HBV infection has been explored. For viral factors, hepatitis B viral load is a strong predictor for liver disease progression. Hepatitis B viral kinetics appear to be important for successful anti-viral therapy. Serum HBsAg level serves as a complementary marker to viral load for the prediction of HBV-related adverse outcomes in patients with low viral load. In those with low viral load, high serum HBsAg level is associated with higher risks of cirrhosis and HCC...
December 2016: Clinical and Molecular Hepatology
https://www.readbyqxmd.com/read/28079935/regional-heritability-mapping-and-genome-wide-association-identify-loci-for-complex-growth-wood-and-disease-resistance-traits-in-eucalyptus
#16
Rafael Tassinari Resende, Marcos Deon Vilela Resende, Fabyano Fonseca Silva, Camila Ferreira Azevedo, Elizabete Keiko Takahashi, Orzenil Bonfim Silva-Junior, Dario Grattapaglia
Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K...
February 2017: New Phytologist
https://www.readbyqxmd.com/read/28079285/a-pathway-based-association-study-reveals-variants-from-wnt-signaling-genes-contributing-to-asthma-susceptibility
#17
A Barreto-Luis, A Corrales, M Acosta-Herrera, C Gonzalez-Colino, J Cumplido, J Martinez-Tadeo, A Carracedo, J Villar, T Carrillo, M Pino-Yanes, C Flores
BACKGROUND: Genetic susceptibility to asthma is currently linked to a handful of genes which have a limited ability to predict the overall disease risk, suggesting the existence of many other genes involved in disease development. Accumulated evidence from association studies in genes related by biological pathways could reveal novel asthma genes. OBJECTIVE: To reveal novel asthma susceptibility genes by means of a pathway-based association study. METHODS: Based on summary data from a previous a genome-wide association study (GWAS) of asthma, we first identified significant biological pathways using a gene-set enrichment analysis...
January 12, 2017: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28073065/in-silico-approach-to-identify-non-synonymous-snps-in-human-obesity-related-gene-mc3r-melanocortin-3-receptor
#18
Rajan Kumar Singh, Kulandaivelu Mahalingam
The melanocortin-3-receptor (MC3R) is a novel gene candidate for human obesity, which involved in controlling the energy homeostasis and food intake behavior. The main aim behind this work is to investigate the potentially deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in obesity related gene MC3R by using six computational tools viz., PolyPhen, I-Mutant, PROVEAN, SIFT, PANTHER and PhD-SNP. In our study, we predicted eight nsSNPs i.e., rs74315393 (Ile146Asn), rs368205448 (Asp121Tyr), rs143321797 (Phe45Ser), rs17847261 (Cys274Ser), rs144166442 (Pro257His), rs370533946 (Leu224Pro), rs371354428 (Pro72Leu) and rs373708098 (Gly249Ser) found to be potentially deleterious...
December 29, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28072499/in-silico-analysis-of-the-deleterious-nssnp-s-missense-in-the-homeobox-domain-of-human-hoxb13-gene-responsible-for-hereditary-prostate-cancer
#19
Gopalakrishnan Chandrasekaran, Eu Chang Hwang, Taek Won Kang, Dongdeuk Kwon, Kwangsung Park, Je-Jung Lee, Vinoth-Kumar Lakshmanan
The human HOXB13 gene encodes a transcription factor containing a DNA-binding homeobox domain and a HoxA13 N-terminal domain. SNP is considered to be the primary genetic cause for hereditary prostate cancer (PCa). The study of functional nsSNP's would give an insight into the exact cause underlying the onset of hereditary PCa and possible methodologies for the cure or early management of the disease. Several in silico tools were used to screen and map the deleterious nsSNP's to the protein structure for predicting the structure-function effects...
January 10, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28070610/automated-tetraploid-genotype-calling-by-hierarchical-clustering
#20
Cari A Schmitz Carley, Joseph J Coombs, David S Douches, Paul C Bethke, Jiwan P Palta, Richard G Novy, Jeffrey B Endelman
New software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall...
January 9, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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