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https://www.readbyqxmd.com/read/29352395/association-between-crp-genetic-diversity-and-bipolar-disorder-comorbid-complications
#1
Wahid Boukouaci, José Oliveira, Bruno Etain, Meriem Bennabi, Christina Mariaselvam, Nora Hamdani, Céline Manier, Djaouida Bengoufa, Frank Bellivier, Chantal Henry, Jean-Pierre Kahn, Dominique Charron, Rajagopal Krishnamoorthy, Marion Leboyer, Ryad Tamouza
BACKGROUND: Chronic low-grade inflammation is believed to contribute, at least in a subset of patients, to the development of bipolar disorder (BD). In this context, the most investigated biological marker is the acute phase response molecule, C-reactive protein (CRP). While the genetic diversity of CRP was amply studied in various pathological settings, little is known in BD. METHODS: 568 BD patients along with 163 healthy controls (HC) were genotyped for the following single-nucleotide polymorphisms (SNPs) on the CRP gene: intron rs1417938 (+ 29) T/A, 3'-UTR rs1130864 (+ 1444) G/A, and downstream rs1205 (+ 1846) (C/T)...
January 20, 2018: International Journal of Bipolar Disorders
https://www.readbyqxmd.com/read/29352185/genetic-fingerprinting-of-salmon-louse-lepeophtheirus-salmonis-populations-in-the-north-east-atlantic-using-a-random-forest-classification-approach
#2
A Jacobs, M De Noia, K Praebel, Ø Kanstad-Hanssen, M Paterno, D Jackson, P McGinnity, A Sturm, K R Elmer, M S Llewellyn
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29351903/integrative-genomic-analysis-predicts-causative-cis-regulatory-mechanisms-of-the-breast-cancer-associated-genetic-variant-rs4415084
#3
Yi Zhang, Mohith Manjunath, Shilu Zhang, Deborah Chasman, Sushmita Roy, Jun S Song
Previous genome-wide association studies (GWAS) have identified several common genetic variants that may significantly modulate cancer susceptibility. However, the precise molecular mechanisms behind these associations remain largely unknown; it is often not clear whether discovered variants are themselves functional or merely genetically linked to other functional variants. Here we provide an integrated method for identifying functional regulatory variants associated with cancer and their target genes by combining analyses of expression quantitative trait loci (eQTL), a modified version of allele-specific expression (ASE) that systematically utilizes haplotype information, transcription factor (TF) binding preference, and epigenetic information...
January 19, 2018: Cancer Research
https://www.readbyqxmd.com/read/29348129/genomic-cdkn2a-2b-deletions-in-adult-ph-all-are-adverse-despite-allogeneic-stem-cell-transplantation
#4
Heike Pfeifer, Katharina Raum, Sandra Markovic, Verena Nowak, Stephanie Fey, Julia Obländer, Jovita Pressler, Verena Böhm, Monika Brüggemann, Lydia Wunderle, Andreas Hüttmann, Ralph Wäsch, Joachim Beck, Matthias Stelljes, Andreas Viardot, Fabian Lang, Dieter Hoelzer, Wolf-Karsten Hofmann, Hubert Serve, Christel Weiss, Nicola Goekbuget, Oliver G Ottmann, Daniel Nowak
We investigated the role of copy number alterations to refine risk stratification in adult Philadelphia chromosome positive (Ph)+ ALL treated with tyrosine kinase inhibitors (TKI) and allogeneic stem cell transplantation (aSCT). 97 Ph+ ALL patients (median age 41 years, range 18-64 years) within the prospective multicenter GMALL studies 06/99 (n=8) and 07/2003 (n=89) were analysed. All patients received TKI and aSCT in first complete remission (CR1). Copy number analysis was performed with SNP arrays and validated by multiplex ligation-dependent probe amplification (MLPA)...
January 18, 2018: Blood
https://www.readbyqxmd.com/read/29346471/use-of-single-nucleotide-polymorphisms-and-mammographic-density-plus-classic-risk-factors-for-breast-cancer-risk-prediction
#5
Elke M van Veen, Adam R Brentnall, Helen Byers, Elaine F Harkness, Susan M Astley, Sarah Sampson, Anthony Howell, William G Newman, Jack Cuzick, D Gareth R Evans
Importance: Single-nucleotide polymorphisms (SNPs) have demonstrated an association with breast cancer susceptibility, but there is limited evidence on how to incorporate them into current breast cancer risk prediction models. Objective: To determine whether a panel of 18 SNPs (SNP18) may be used to predict breast cancer in combination with classic risk factors and mammographic density. Design, Setting, and Participants: This cohort study enrolled a subcohort of 9363 women, aged 46 to 73 years, without a previous breast cancer diagnosis from the larger prospective cohort of the PROCAS study (Predicting Risk of Cancer at Screening) specifically to evaluate breast cancer risk-assessment methods...
January 18, 2018: JAMA Oncology
https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#6
Wubishet A Bekele, Charlene P Wight, Shiaoman Chao, Catherine J Howarth, Nicholas A Tinker
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel...
January 18, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29345073/improving-accuracy-of-genomic-prediction-in-brangus-cattle-by-adding-animals-with-imputed-low-density-snp-genotypes
#7
F B Lopes, X-L Wu, H Li, J Xu, T Perkins, J Genho, R Ferretti, R G Tait, S Bauck, G J M Rosa
Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled...
February 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29343235/comparison-of-three-assembly-strategies-for-a-heterozygous-seedless-grapevine-genome-assembly
#8
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29340733/population-pharmacokinetics-of-lamotrigine-co-administered-with-valproic-acid-in-chinese-epileptic-children-using-nonlinear-mixed-effects-modeling
#9
Shansen Xu, Limin Liu, Yanan Chen, Mei Liu, Tong Lu, Huanxin Wang, Shihao Liu, Mingming Zhao, Limei Zhao
PURPOSE: The aims of this study were to develop a population pharmacokinetic (PPK) model of lamotrigine (LTG) in Chinese epileptic children by using nonlinear mixed effects modeling (NONMEM) and to investigate the effects of valproic acid (VPA) and genetic polymorphisms of the major metabolizing enzymes (UGT1A4, UGT2B7) on the pharmacokinetics of LTG. METHODS: A total of 182 epileptic children who were treated with LTG as monotherapy or as part of combination therapy were included in this study as the model group, and 61 patients were included as the validation group...
January 16, 2018: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29340111/effect-of-dihydropyrimidine-dehydrogenase-single-nucleotide-polymorphisms-on-prognosis-of-breast-cancer-patients-with-chemotherapy
#10
Fengxia Qin, Huikun Zhang, Yong Huang, Limin Yang, Feng Yu, Xiaoli Liu, Li Fu, Feng Gu, Yongjie Ma
Defining biomarkers that predict therapeutic effects and adverse events is a crucial mandate to guide patient selection for personalized cancer treatments. DPD (dihydropyrimidine dehydrogenase, encoded by DPYD gene) is the initial and rate-limiting enzyme of metabolic pathway of fluoropyrimidines, and fluoropyrimidines are common used drug therapies for breast cancer. Previous studies on DPYD polymorphism were mainly focused on its association with fluoropyrimidines toxicity. In our present study, 5 DPYD single nucleotide polymorphisms status was detected from tumor tissues of 331 invasive breast cancer patients using standard techniques...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340022/a-functional-polymorphism-of-ssbp1-gene-predicts-prognosis-and-response-to-chemotherapy-in-resected-gastric-cancer-patients
#11
Qiuchen Li, Falin Qu, Renli Li, Xianli He, Yulong Zhai, Weigang Chen, Yong Zheng
Growing evidence has indicated that single-stranded DNA-binding proteins 1 (SSBP1) is involved in tumor initiation and progression. However, effects of single nucleotide polymorphisms (SNPs) in SSBP1 gene on gastric cancer (GC) prognosis are still unknown. In present study, two functional SNPs from SSBP1 were selected and genotyped in a large cohorts of 1030 resected GC patients (326 in the training set, 704 in the validation set) to explore the association of SNPs with patients' survival. The rs6976500 G allele (CG/GG) genotypes were found significantly associated with both worse overall survival (OS) and recurrence-free survival (RFS) in the training and the independent validation set when compared to C allele genotype, which reaching a more robust statistical significance in the pooled analysis...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29338921/faster-progression-from-mci-to-probable-ad-for-carriers-of-a-single-nucleotide-polymorphism-associated-with-type-2-diabetes
#12
Hugo Girard, Olivier Potvin, Scott Nugent, Caroline Dallaire-Théroux, Stephen Cunnane, Simon Duchesne
Sporadic Alzheimer's disease (AD), as opposed to its autosomal dominant form, is likely caused by a complex interaction of genetic, environmental, and health lifestyle factors. Twin studies indicate that sporadic AD heritability could be between 58% and 79%, around half of which is explained by the ε4 allele of the apolipoprotein E (APOE4). We hypothesized that genes associated with known risk factors for AD, namely hypertension, hypercholesterolemia, obesity, diabetes, and cardiovascular disease, would contribute significantly to the remaining heritability...
December 7, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29338102/circulating-serum-25-hydroxyvitamin-d-levels-and-bone-mineral-density-mendelian-randomization-study
#13
Susanna C Larsson, Håkan Melhus, Karl Michaëlsson
There is considerable discussion of the importance for increased serum 25-hydroxyvitamin D (S-25OHD) concentration associated with adequacy for bone health. Accordingly, whether long-term high S-25OHD concentration in general positively affects bone mineral density (BMD) is uncertain. We used a Mendelian randomization design to determine the association between genetically increased S-25OHD concentrations and BMD. Five single-nucleotide polymorphisms (SNPs) in or near genes encoding enzymes and carrier proteins involved in vitamin D synthesis or metabolism were used as instrumental variables to genetically predict one standard deviation increase in S-25OHD concentration...
January 16, 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/29336255/fast-screening-technology-for-drug-emergency-management-predicting-suspicious-snps-for-adr-with-information-theory-based-models
#14
Zhaohui Liang, Jun Liu, Jimmy Xiangji Huang, Xing Zeng
OBJECTIVE: The genetic polymorphism of Cytochrome P450 (CYP 450) is considered as one of the main causes for adverse drug reactions (ADRs). In order to explore the latent correlations between ADRs and potentially corresponding single-nucleotide polymorphism (SNPs) in CYP450, three algorithms based on information theory are used as the main method to predict the possible relation. METHODS: The study uses a retrospective case-control study to explore the potential relation of ADRs to specific genomic locations and single-nucleotide polymorphism (SNP)...
January 14, 2018: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/29335276/assigning-function-to-natural-allelic-variation-via-dynamic-modeling-of-gene-network-induction
#15
Magali Richard, Florent Chuffart, Hélène Duplus-Bottin, Fanny Pouyet, Martin Spichty, Etienne Fulcrand, Marianne Entrevan, Audrey Barthelaix, Michael Springer, Daniel Jost, Gaël Yvert
More and more natural DNA variants are being linked to physiological traits. Yet, understanding what differences they make on molecular regulations remains challenging. Important properties of gene regulatory networks can be captured by computational models. If model parameters can be "personalized" according to the genotype, their variation may then reveal how DNA variants operate in the network. Here, we combined experiments and computations to visualize natural alleles of the yeast GAL3 gene in a space of model parameters describing the galactose response network...
January 15, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29334686/fat-mass-and-obesity-related-gene-variants-rs9939609-and-rs7185735-are-associated-with-second-generation-antipsychotic-induced-weight-gain
#16
Charlotte Schröder, Fabian Czerwensky, Stefan Leucht, Werner Steimer
INTRODUCTION: Weight gain is a limiting and frequent adverse effect of second-generation antipsychotic therapy. Identifying genetic risk factors would significantly improve pharmacotherapy. METHODS: We focused on rs7185735 and rs9939609, 2 common single nucleotide polymorphisms of the fat mass and obesity-associated (FTO) gene reported to be associated with obesity. Three-hundred fifty Caucasian inpatients were included in a naturalistic study. RESULTS: After 4 weeks of treatment, we did not observe any significant association of polymorphisms with weight change in the whole study population (p>0...
January 15, 2018: Pharmacopsychiatry
https://www.readbyqxmd.com/read/29332452/the-dnmt3b-579g-t-polymorphism-is-significantly-associated-with-the-risk-of-gastric-cancer-but-not-lung-cancer-in-chinese-population
#17
Bifeng Chen, Jingdong Wang, Xiuli Gu, Jingli Zhang, Jiankun Zhang, Xianhong Feng
The -149C>T and -579G>T, 2 single nucleotide polymorphisms in de novo methyltransferase 3B gene promoter, have been previously reported to potentially alter the promoter activity and to influence cancer risk. However, the results from previous studies remain conflicting rather than conclusive. In view of this, we conducted a case-control study and then a meta-analysis to examine the association between these 2 single-nucleotide polymorphisms with risk of lung and gastric cancer in Chinese population. The genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism and confirmed by sequencing...
December 2017: Technology in Cancer Research & Treatment
https://www.readbyqxmd.com/read/29330500/integration-of-gwas-pathway-and-network-analyses-reveals-novel-mechanistic-insights-into-the-synthesis-of-milk-proteins-in-dairy-cows
#18
Sara Pegolo, Núria Mach, Yuliaxis Ramayo-Caldas, Stefano Schiavon, Giovanni Bittante, Alessio Cecchinato
The quantities and proportions of protein fractions have notable effects on the nutritional and technological value of milk. Although much is known about the effects of genetic variants on milk proteins, the complex relationships among the set of genes and pathways regulating the different protein fractions synthesis and secretion into milk in dairy cows are still not completely understood. We conducted genome-wide association studies (GWAS) for milk nitrogen fractions in a cohort of 1,011 Brown Swiss cows, which uncovered 170 significant single nucleotide polymorphism (SNPs), mostly located on BTA6 and BTA11...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29327717/combined-mutation-and-copy-number-variation-detection-by-targeted-next-generation-sequencing-in-uveal-melanoma
#19
Kyra N Smit, Natasha M van Poppelen, Jolanda Vaarwater, Robert Verdijk, Ronald van Marion, Helen Kalirai, Sarah E Coupland, Sophie Thornton, Neil Farquhar, Hendrikus-Jan Dubbink, Dion Paridaens, Annelies de Klein, Emine Kiliç
Uveal melanoma is a highly aggressive cancer of the eye, in which nearly 50% of the patients die from metastasis. It is the most common type of primary eye cancer in adults. Chromosome and mutation status have been shown to correlate with the disease-free survival. Loss of chromosome 3 and inactivating mutations in BAP1, which is located on chromosome 3, are strongly associated with 'high-risk' tumors that metastasize early. Other genes often involved in uveal melanoma are SF3B1 and EIF1AX, which are found to be mutated in intermediate- and low-risk tumors, respectively...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29326435/a-combined-analysis-of-genetically-correlated-traits-identifies-187-loci-and-a-role-for-neurogenesis-and-myelination-in-intelligence
#20
W D Hill, R E Marioni, O Maghzian, S J Ritchie, S P Hagenaars, A M McIntosh, C R Gale, G Davies, I J Deary
Intelligence, or general cognitive function, is phenotypically and genetically correlated with many traits, including a wide range of physical, and mental health variables. Education is strongly genetically correlated with intelligence (r g  = 0.70). We used these findings as foundations for our use of a novel approach-multi-trait analysis of genome-wide association studies (MTAG; Turley et al. 2017)-to combine two large genome-wide association studies (GWASs) of education and intelligence, increasing statistical power and resulting in the largest GWAS of intelligence yet reported...
January 11, 2018: Molecular Psychiatry
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