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https://www.readbyqxmd.com/read/28227132/effect-specific-analysis-of-pathogenic-snvs-in-human-interactome-leveraging-edge-based-network-robustness
#1
Hongzhu Cui, Dmitry Korkin, Hongzhu Cui, Dmitry Korkin, Dmitry Korkin, Hongzhu Cui
Study of genetic variants in the context of molecular networks has recently gained much attention. However, many of these studies suffer from the lack of functional information about the network rewiring effect of genetic variants. After large-scale homology modeling, plus extracting native structure from PDB database, we performed structure-based prediction about the rewiring effect using our SNP-IN tool, and it covers significantly more variants than experimental characterization. The analysis result confirms the widespread perturbations in human interactome and reveals the network rewiring behavior based on edge-based network robustness concept...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28223462/fallacy-of-the-unique-genome-sequence-diversity-within-single-helicobacter-pylori-strains
#2
Jenny L Draper, Lori M Hansen, David L Bernick, Samar Abedrabbo, Jason G Underwood, Nguyet Kong, Bihua C Huang, Allison M Weis, Bart C Weimer, Arnoud H M van Vliet, Nader Pourmand, Jay V Solnick, Kevin Karplus, Karen M Ottemann
Many bacterial genomes are highly variable but nonetheless are typically published as a single assembled genome. Experiments tracking bacterial genome evolution have not looked at the variation present at a given point in time. Here, we analyzed the mouse-passaged Helicobacter pylori strain SS1 and its parent PMSS1 to assess intra- and intergenomic variability. Using high sequence coverage depth and experimental validation, we detected extensive genome plasticity within these H. pylori isolates, including movement of the transposable element IS607, large and small inversions, multiple single nucleotide polymorphisms, and variation in cagA copy number...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28222685/evaluation-of-the-accuracy-of-imputed-sequence-variant-genotypes-and-their-utility-for-causal-variant-detection-in-cattle
#3
Hubert Pausch, Iona M MacLeod, Ruedi Fries, Reiner Emmerling, Phil J Bowman, Hans D Daetwyler, Michael E Goddard
BACKGROUND: The availability of dense genotypes and whole-genome sequence variants from various sources offers the opportunity to compile large datasets consisting of tens of thousands of individuals with genotypes at millions of polymorphic sites that may enhance the power of genomic analyses. The imputation of missing genotypes ensures that all individuals have genotypes for a shared set of variants. RESULTS: We evaluated the accuracy of imputation from dense genotypes to whole-genome sequence variants in 249 Fleckvieh and 450 Holstein cattle using Minimac and FImpute...
February 21, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28217400/novel-plasma-biomarker-of-atenolol-induced-hyperglycemia-identified-through-a-metabolomics-genomics-integrative-approach
#4
Felipe A de Oliveira, Mohamed H Shahin, Yan Gong, Caitrin W McDonough, Amber L Beitelshees, John G Gums, Arlene B Chapman, Eric Boerwinkle, Stephen T Turner, Reginald F Frye, Oliver Fiehn, Rima Kaddurah-Daouk, Julie A Johnson, Rhonda M Cooper-DeHoff
INTRODUCTION: While atenolol is an effective antihypertensive agent, its use is also associated with adverse events including hyperglycemia and incident diabetes that may offset the benefits of blood pressure lowering. By combining metabolomic and genomic data acquired from hypertensive individuals treated with atenolol, it may be possible to better understand the pathways that most impact the development of an adverse glycemic state. OBJECTIVE: To identify biomarkers that can help predict susceptibility to blood glucose excursions during exposure to atenolol...
August 2016: Metabolomics: Open Access
https://www.readbyqxmd.com/read/28215537/genetic-variations-of-mitochondrial-genome-modify-risk-and-prognosis-of-hepatocellular-carcinoma-patients
#5
Cheng Chen, Yanna Ba, Deyang Li, Xiaohong Du, Xin Lia, Hai Yang, Jiaze An, Jinliang Xing, Hushan Yang, Guanglong Dong, Xu Guo
BACKGROUND: Previous studies have indicated that mitochondrial genetic variations were associated with the risk of many cancers. However, there are few reports on the association between single nucleotide polymorphisms (SNPs) or haplogroups of mitochondrial DNA (mtDNA) and the risk or prognosis of hepatocellular carcinoma (HCC). METHODS: In order to investigate the predictive and prognostic role of mtDNA SNPs and haplogroups in HCC, the mitochondrial genome of 188 HCC patients and 344 healthy controls were sequenced by next generation sequencing technology...
February 16, 2017: Clinics and Research in Hepatology and Gastroenterology
https://www.readbyqxmd.com/read/28214980/sil2r-ratio-as-early-marker-for-response-in-hairy-cell-leukemia-and-the-prognostic-relevance-of-il28b-genotype-to-interferon-%C3%AE-therapy
#6
Stéphanie Jud, Jeroen S Goede, Oliver Senn, Katharina Spanaus, Markus G Manz, Rudolf Benz
Interferon-α (IFNα) was the first effective drug therapy for hairy cell leukemia (HCL). Nowadays, it is used as an alternative treatment in selected patients. Due to unlimited treatment time, monitoring and early prediction of response are important. Moreover, IFNα is used in the therapy of chronic hepatitis C, where a single nucleotide polymorphism of interleukin-28B gene (IL28B) correlates with therapy response. The role of this polymorphism in therapy response of IFNα-treated patients with HCL is unknown...
February 18, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28214693/genomic-prediction-for-beef-fatty-acid-profile-in-nellore-cattle
#7
Hermenegildo Lucas Justino Chiaia, Elisa Peripoli, Rafael Medeiros de Oliveira Silva, Carolyn Aboujaoude, Fabiele Loise Braga Feitosa, Marcos Vinicius Antunes de Lemos, Mariana Piatto Berton, Bianca Ferreira Olivieri, Rafael Espigolan, Rafael Lara Tonussi, Daniel Gustavo Mansan Gordo, Tiago Bresolin, Ana Fabrícia Braga Magalhães, Gerardo Alves Fernandes Júnior, Lúcia Galvão de Albuquerque, Henrique Nunes de Oliveira, Joyce de Jesus Mangini Furlan, Adrielle Mathias Ferrinho, Lenise Freitas Mueller, Humberto Tonhati, Angélica Simone Cravo Pereira, Fernando Baldi
The objective of this study was to compare SNP-BLUP, BayesCπ, BayesC and Bayesian Lasso methodologies to predict the direct genomic value for saturated, monounsaturated, and polyunsaturated fatty acid profile, omega 3 and 6 in the Longissimus thoracis muscle of Nellore cattle finished in feedlot. A total of 963 Nellore bulls with phenotype for fatty acid profiles, were genotyped using the Illumina BovineHD BeadChip (Illumina, San Diego, CA) with 777,962 SNP. The predictive ability was evaluated using cross validation...
February 9, 2017: Meat Science
https://www.readbyqxmd.com/read/28213955/the-skin-barrier-function-gene-spink5-is-associated-with-challenge-proven-ige-mediated-food-allergy-in-infants
#8
Sarah E Ashley, Hern-Tze Tina Tan, Peter Vuillermin, Shyamali C Dharmage, Mimi L K Tang, Jennifer Koplin, Lyle C Gurrin, Adrian Lowe, Caroline Lodge, Anne-Louise Ponsonby, John Molloy, Pamela Martin, Melanie C Matheson, Richard Saffery, Katrina J Allen, Justine A Ellis, David Martino
BACKGROUND: A defective skin barrier is hypothesised to be an important route of sensitisation to dietary antigens, and may lead to food allergy in some children. Missense mutations in the Serine peptidase inhibitor kazal type 5 (SPINK5) skin barrier gene have previously been associated with allergic conditions. OBJECTIVE: To determine whether genetic variants in and around SPINK5 are associated with IgE mediated food allergy. METHOD: We genotyped 71 'tag' single nucleotide polymorphisms (tag-SNPs) within a region spanning ~263 kilobases (kb) including SPINK5 (~61kb) in n=722 (n=367 food allergic, n=199 food sensitised, tolerant and n=156 non-food allergic controls) 12-month infants (discovery sample) phenotyped for food allergy with the gold standard oral food challenge (OFC)...
February 18, 2017: Allergy
https://www.readbyqxmd.com/read/28213371/polygenic-risk-scores-in-familial-alzheimer-disease
#9
Giuseppe Tosto, Thomas D Bird, Debby Tsuang, David A Bennett, Bradley F Boeve, Carlos Cruchaga, Kelley Faber, Tatiana M Foroud, Martin Farlow, Alison M Goate, Sarah Bertlesen, Neill R Graff-Radford, Martin Medrano, Rafael Lantigua, Jennifer Manly, Ruth Ottman, Roger Rosenberg, Daniel J Schaid, Nicole Schupf, Yaakov Stern, Robert A Sweet, Richard Mayeux
OBJECTIVE: To investigate the association between a genetic risk score (GRS) and familial late-onset Alzheimer disease (LOAD) and its predictive value in families multiply affected by the disease. METHODS: Using data from the National Institute on Aging Genetics Initiative for Late-Onset Alzheimer Disease (National Institute on Aging-Late-Onset Alzheimer's Disease Family Study), mixed regression models tested the association of familial LOAD with a GRS based on single nucleotide polymorphisms (SNPs) previously associated with LOAD...
February 17, 2017: Neurology
https://www.readbyqxmd.com/read/28212671/an-adaptive-variant-of-trib2-rs1057001-is-associated-with-higher-expression-levels-of-thermogenic-genes-in-human-subcutaneous-and-visceral-adipose-tissues
#10
Kazuhiro Nakayama, Sadahiko Iwamoto
BACKGROUND: An obesity-related single-nucleotide polymorphism (SNP) of the Tribbles pseudokinase 2 gene (TRIB2) was shown to have underwent adaptive evolution in the last glacial period, suggesting a selective advantage of this SNP in human populations in cold environments. In order to verify this hypothesis, the effect of the TRIB2 SNP on the expression of genes involved in adaptive thermogenesis was tested using messenger RNAs prepared from adipose tissues of Japanese adults. METHODS: Complementary DNA was prepared from subcutaneous adipose tissues (SAT) and visceral adipose tissues (VAT) obtained from 48 Japanese adults...
February 17, 2017: Journal of Physiological Anthropology
https://www.readbyqxmd.com/read/28211463/ecological-and-genetic-basis-of-metapopulation-persistence-of-the-glanville-fritillary-butterfly-in-fragmented-landscapes
#11
Ilkka Hanski, Torsti Schulz, Swee Chong Wong, Virpi Ahola, Annukka Ruokolainen, Sami P Ojanen
Ecologists are challenged to construct models of the biological consequences of habitat loss and fragmentation. Here, we use a metapopulation model to predict the distribution of the Glanville fritillary butterfly during 22 years across a large heterogeneous landscape with 4,415 small dry meadows. The majority (74%) of the 125 networks into which the meadows were clustered are below the extinction threshold for long-term persistence. Among the 33 networks above the threshold, spatial configuration and habitat quality rather than the pooled habitat area predict metapopulation size and persistence, but additionally allelic variation in a SNP in the gene Phosphoglucose isomerase (Pgi) explains 30% of variation in metapopulation size...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28207977/adaptation-of-the-pathogen-pseudomonas-syringae-during-experimental-evolution-on-a-native-versus-alternative-host-plant
#12
Sean Meaden, Britt Koskella
The specialization and distribution of pathogens among species has substantial impact on disease spread, especially when reservoir hosts can maintain high pathogen densities or select for increased pathogen virulence. Theory predicts that optimal within-host growth rate will vary among host genotypes/species, and therefore that pathogens infecting multiple hosts should experience different selection pressures depending on the host environment in which they are found. This should be true for pathogens with broad host ranges, but also those experiencing opportunistic infections on novel hosts or that spill over among host populations...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28205206/apples-and-oranges-four-definitions-of-multiple-chronic-conditions-and-their-relationship-to-30-day-hospital-readmission
#13
Melissa Dattalo, Eva DuGoff, Katie Ronk, Korey Kennelty, Andrea Gilmore-Bykovskyi, Amy J Kind
OBJECTIVES: To determine the extent of agreement between four commonly used definitions of multiple chronic conditions (MCCs) and compare each definition's ability to predict 30-day hospital readmissions. DESIGN: Retrospective cohort study. SETTING: National Medicare claims data. PARTICIPANTS: Random sample of Medicare beneficiaries discharged from the hospital from 2005 to 2009 (n = 710,609). MEASUREMENTS: Baseline chronic conditions were determined for each participant using four definitions of MCC...
February 15, 2017: Journal of the American Geriatrics Society
https://www.readbyqxmd.com/read/28202046/highly-predictive-snp-markers-for-efficient-selection-of-the-wheat-leaf-rust-resistance-gene-lr16
#14
Mulualem T Kassa, Frank M You, Colin W Hiebert, Curtis J Pozniak, Pierre R Fobert, Andrew G Sharpe, James G Menzies, D Gavin Humphreys, Nicole Rezac Harrison, John P Fellers, Brent D McCallum, Curt A McCartney
BACKGROUND: Lr16 is a widely deployed leaf rust resistance gene in wheat (Triticum aestivum L.) that is highly effective against the North American Puccinia triticina population when pyramided with the gene Lr34. Lr16 is a seedling leaf rust resistance gene conditioning an incompatible interaction with a distinct necrotic ring surrounding the uredinium. Lr16 was previously mapped to the telomeric region of the short arm of wheat chromosome 2B. The goals of this study were to develop numerous single nucleotide polymorphism (SNP) markers for the Lr16 region and identify diagnostic gene-specific SNP marker assays for marker-assisted selection (MAS)...
February 15, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28202015/variant-discovery-in-the-sheep-milk-transcriptome-using-rna-sequencing
#15
Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser-Klopp, Juan José Arranz
BACKGROUND: The identification of genetic variation underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing (RNA-Seq) offers new opportunities for the detection of transcriptome variants (SNPs and short indels) in different tissues and species. In this study, we used RNA-Seq on Milk Sheep Somatic Cells (MSCs) with the goal of characterizing the genetic variation within the coding regions of the milk transcriptome in Churra and Assaf sheep, two common dairy sheep breeds farmed in Spain...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198815/enhancing-genomic-prediction-with-genome-wide-association-studies-in-multiparental-maize-populations
#16
Y Bian, J B Holland
Genome-wide association mapping using dense marker sets has identified some nucleotide variants affecting complex traits that have been validated with fine-mapping and functional analysis. However, many sequence variants associated with complex traits in maize have small effects and low repeatability. In contrast to genome-wide association study (GWAS), genomic prediction (GP) is typically based on models incorporating information from all available markers, rather than modeling effects of individual loci. We considered methods to integrate results of GWASs into GP models in the context of multiple interconnected families...
February 15, 2017: Heredity
https://www.readbyqxmd.com/read/28198095/genetic-risk-models-influence-of-model-size-on-risk-estimates-and-precision
#17
Ying Shan, Gerard Tromp, Helena Kuivaniemi, Diane T Smelser, Shefali S Verma, Marylyn D Ritchie, James R Elmore, David J Carey, Yvette P Conley, Michael B Gorin, Daniel E Weeks
Disease risk estimation plays an important role in disease prevention. Many studies have found that the ability to predict risk improves as the number of risk single-nucleotide polymorphisms (SNPs) in the risk model increases. However, the width of the confidence interval of the risk estimate is often not considered in the evaluation of the risk model. Here, we explore how the risk and the confidence interval width change as more SNPs are added to the model in the order of decreasing effect size, using both simulated data and real data from studies of abdominal aortic aneurysms and age-related macular degeneration...
February 15, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28195643/clinical-and-genetic-predictors-of-weight-gain-in-patients-diagnosed-with-breast-cancer
#18
Maureen Sadim, Yanfei Xu, Katharina Selig, Julie Paulus, Regina Uthe, Surbhi Agarwl, Iram Dubin, Panagiota Oikonomopoulou, Lesya Zaichenko, Silvia Aki McCandlish, Linda Van Horn, Christos Mantzoros, Donna Pauler Ankerst, Virginia G Kaklamani
BACKGROUND: Postdiagnosis weight gain in patients with breast cancer has been associated with increased cancer recurrence and mortality. This study was designed to identify risk factors for weight gain and create a predictive model to identify a high-risk population for targeted interventions. METHODS: The weight of 393 patients with breast cancer from the Northwestern Robert H. Lurie Cancer Center was measured over a 2-year period from diagnosis, with body mass index (BMI) change over 18 months as the primary endpoint...
February 14, 2017: Cancer
https://www.readbyqxmd.com/read/28193567/genomic-analysis-of-adult-b-all-identifies-potential-markers-of-shorter-survival
#19
Shiven Patel, Clinton C Mason, Martha J Glenn, Christian N Paxton, Sara T South, Melissa H Cessna, Julie Asch, Erin F Cobain, Dale L Bixby, Lauren B Smith, Shalini Reshmi, Julie M Gastier-Foster, Joshua D Schiffman, Rodney R Miles
B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL, but data regarding genetic prognostic biomarkers are much more limited for adult patients. We identified 70 adult B-ALL patients from three institutions and performed genome-wide analysis via single nucleotide polymorphism (SNP) arrays on DNA isolated from their initial diagnostic sample and, when available, relapse bone marrow specimens to identify recurring copy number alterations (CNA)...
February 3, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28193175/genome-wide-association-mapping-for-milk-fat-composition-and-fine-mapping-of-a-qtl-for-de-novo-synthesis-of-milk-fatty-acids-on-bovine-chromosome-13
#20
Hanne Gro Olsen, Tim Martin Knutsen, Achim Kohler, Morten Svendsen, Lars Gidskehaug, Harald Grove, Torfinn Nome, Marte Sodeland, Kristil Kindem Sundsaasen, Matthew Peter Kent, Harald Martens, Sigbjørn Lien
BACKGROUND: Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle...
February 13, 2017: Genetics, Selection, Evolution: GSE
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