keyword
MENU ▼
Read by QxMD icon Read
search

Prediction snp

keyword
https://www.readbyqxmd.com/read/29785925/comparison-of-two-genotyping-methods-for-distinguishing-recrudescence-from-reinfection-in-antimalarial-drug-efficacy-effectiveness-trials
#1
Joseph R M Fulakeza, Rachel L Banda, Trancizeo R Lipenga, Dianne J Terlouw, Standwell C Nkhoma, Eva Maria Hodel
Genotyping of allelic variants of Plasmodium falciparum merozoite surface proteins 1 and 2 ( msp-1 and msp-2 ), and the glutamate-rich protein is the gold standard for distinguishing reinfections from recrudescences in antimalarial drug trials. We compared performance of the recently developed 24-single-nucleotide polymorphism (SNP) Barcoding Assay against msp-1 and msp-2 genotyping in a cluster-randomized effectiveness trial of artemether-lumefantrine and dihydroartemisinin-piperaquine in Malawi. Rates of recrudescence and reinfection estimated by the two methods did not differ significantly (Fisher's exact test; P = 0...
May 21, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29784573/phactr1-genotype-predicts-coronary-artery-disease-in-patients-with-familial-hypercholesterolemia
#2
Martine Paquette, Robert Dufour, Alexis Baass
BACKGROUND: Familial hypercholesterolemia (FH) is the most frequent autosomal codominant disease worldwide and is characterized by elevated low-density lipoprotein cholesterol and premature coronary artery disease (CAD). Polymorphisms in phosphatase and actin regulator 1 (PHACTR1) have been shown to be associated with cardiovascular risk in large genome-wide association studies studies. OBJECTIVE: The aim of the present study is to evaluate the association between the rs12526453 polymorphism in the PHACTR1 gene and the prevalence of CAD in FH patients...
April 30, 2018: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/29784544/classifying-alzheimer-s-disease-with-brain-imaging-and-genetic-data-using-a-neural-network-framework
#3
Kaida Ning, Bo Chen, Fengzhu Sun, Zachary Hobel, Lu Zhao, Will Matloff, Arthur W Toga
A long-standing question is how to best use brain morphometric and genetic data to distinguish Alzheimer's disease (AD) patients from cognitively normal (CN) subjects and to predict those who will progress from mild cognitive impairment (MCI) to AD. Here, we use a neural network (NN) framework on both magnetic resonance imaging-derived quantitative structural brain measures and genetic data to address this question. We tested the effectiveness of NN models in classifying and predicting AD. We further performed a novel analysis of the NN model to gain insight into the most predictive imaging and genetics features and to identify possible interactions between features that affect AD risk...
April 24, 2018: Neurobiology of Aging
https://www.readbyqxmd.com/read/29783940/small-rna-based-prediction-of-hybrid-performance-in-maize
#4
Felix Seifert, Alexander Thiemann, Tobias A Schrag, Dominika Rybka, Albrecht E Melchinger, Matthias Frisch, Stefan Scholten
BACKGROUND: Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783939/a-genome-wide-association-study-reveals-novel-genomic-regions-and-positional-candidate-genes-for-fat-deposition-in-broiler-chickens
#5
Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M Reecy, Thaís Fernanda Godoy, Priscila Anchieta Trevisoli, Maurício E Cantão, Mônica Corrêa Ledur, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Ana Silvia Alves Meira Tavares Moura, Dorian Garrick, Luiz Lehmann Coutinho
BACKGROUND: Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken's carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783161/candidate-gene-analysis-in-the-s%C3%A3-o-paulo-epidemiologic-sleep-study-episono-shows-an-association-of-variant-in-pde4d-and-sleepiness
#6
Victoria M Pak, Diego R Mazzotti, Brendan T Keenan, Camila Hirotsu, Philip Gehrman, Lia Bittencourt, Allan I Pack, Sergio Tufik
INTRODUCTION: Sleepiness and cardiovascular disease share common molecular pathways; thus, genetic risk factors for sleepiness may also predict cardiovascular disease risk. This study explored the associations between subjective sleepiness and single-nucleotide polymorphisms (SNPs) in candidate genes within oxidative stress, inflammatory, and neuronal pathways, which may contribute to sleepiness and downstream cardiovascular disease risk: Cytochrome B-245, Alpha Polypeptide (CYBA), Cytochrome B-245, Beta Polypeptide (CYBB), Neutrophil Cytosolic Factor (NCF2), Tumor Necrosis Factor-Alpha (TNFA), and Phosphodiesterase 4D (PDE4D)...
January 12, 2018: Sleep Medicine
https://www.readbyqxmd.com/read/29776335/using-genomic-relationship-likelihood-for-parentage-assignment
#7
Kim E Grashei, Jørgen Ødegård, Theo H E Meuwissen
BACKGROUND: Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage assignment are exclusion-based (i.e. based on loci that violate Mendelian inheritance) or likelihood-based, assuming independent inheritance of loci. For true parent-offspring relations, genotyping errors cause apparent violations of Mendelian inheritance. Thus, the maximum proportion of such violations must be determined, which is complicated by variable call- and genotype error rates among loci and individuals...
May 18, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29774036/the-pattern-and-distribution-of-induced-mutations-in-j-curcas-using-reduced-representation-sequencing
#8
Fatemeh Maghuly, Stephan Pabinger, Julie Krainer, Margit Laimer
Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29772088/predicting-genotypes-environmental-range-from-genome-environment-associations
#9
Stéphanie Manel, Marco Andrello, Karine Henry, Daphné Verdelet, Aude Darracq, Pierre-Edouard Guerin, Bruno Desprez, Pierre Devaux
Genome-environment association methods aim to detect genetic markers associated with environmental variables. The detected associations are usually analysed separately to identify the genomic regions involved in local adaptation. However, a recent study suggests that single-locus associations can be combined and used in a predictive way to estimate environmental variables for new individuals on the basis of their genotypes. Here, we introduce an original approach to predict the environmental range (values and upper and lower limits) of species genotypes from the genetic markers significantly associated with those environmental variables in an independent set of individuals...
May 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29771388/gwas4d-multidimensional-analysis-of-context-specific-regulatory-variant-for-human-complex-diseases-and-traits
#10
Dandan Huang, Xianfu Yi, Shijie Zhang, Zhanye Zheng, Panwen Wang, Chenghao Xuan, Pak Chung Sham, Junwen Wang, Mulin Jun Li
Genome-wide association studies have generated over thousands of susceptibility loci for many human complex traits, and yet for most of these associations the true causal variants remain unknown. Tissue/cell type-specific prediction and prioritization of non-coding regulatory variants will facilitate the identification of causal variants and underlying pathogenic mechanisms for particular complex diseases and traits. By leveraging recent large-scale functional genomics/epigenomics data, we develop an intuitive web server, GWAS4D (http://mulinlab...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29770559/ethical-legal-and-social-implications-of-forensic-molecular-phenotyping-in-south-africa
#11
Nandi Slabbert, Laura Jane Heathfield
Conventional forensic DNA analysis involves a matching principle, which compares DNA profiles from evidential samples to those from reference samples of known origin. In casework, however, the accessibility to a reference sample is not guaranteed which limits the use of DNA as an investigative tool. This has led to the development of phenotype prediction, which uses SNP analysis to estimate the physical appearance of the sample donor. Physical traits, such as eye, hair and skin colour, have been associated with certain alleles within specific genes involved in the melanogenesis pathways...
May 17, 2018: Developing World Bioethics
https://www.readbyqxmd.com/read/29769521/thirty-loci-identified-for-heart-rate-response-to-exercise-and-recovery-implicate-autonomic-nervous-system
#12
Julia Ramírez, Stefan van Duijvenboden, Ioanna Ntalla, Borbala Mifsud, Helen R Warren, Evan Tzanis, Michele Orini, Andrew Tinker, Pier D Lambiase, Patricia B Munroe
Impaired capacity to increase heart rate (HR) during exercise (ΔHRex ), and a reduced rate of recovery post-exercise (ΔHRrec ) are associated with higher cardiovascular mortality rates. Currently, the genetic basis of both phenotypes remains to be elucidated. We conduct genome-wide association studies (GWASs) for ΔHRex and ΔHRrec in ~40,000 individuals, followed by replication in ~27,000 independent samples, all from UK Biobank. Six and seven single-nucleotide polymorphisms for ΔHRex and ΔHRrec , respectively, formally replicate...
May 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29769070/serum-magnesium-levels-and-risk-of-coronary-artery-disease-mendelian-randomisation-study
#13
Susanna C Larsson, Stephen Burgess, Karl Michaëlsson
BACKGROUND: Observational studies have shown that serum magnesium levels are inversely associated with risk of cardiovascular disease, but whether this association is causal is unknown. We conducted a Mendelian randomisation study to investigate whether serum magnesium levels may be causally associated with coronary artery disease (CAD). METHODS: This Mendelian randomisation analysis is based on summary-level data from the CARDIoGRAMplusC4D consortium's 1000 Genomes-based genome-wide association meta-analysis of 48 studies with a total of 60,801 CAD cases and 123,504 non-cases...
May 17, 2018: BMC Medicine
https://www.readbyqxmd.com/read/29768452/tyrosine-nitration-of-cytosolic-peroxidase-is-probably-triggered-as-a-long-distance-signaling-response-in-sunflower-seedling-cotyledons-subjected-to-salt-stress
#14
Prachi Jain, Satish C Bhatla
Present work focuses on tissue and concentration-dependent effect of nitric oxide (NO) on the modulation of cytosolic peroxidase (POD; EC 1.11.1.7) activity in 2-day old etiolated sunflower (Helianthus annuus L.) seedlings. Exogenously supplied NO (in the form of sodium nitroprusside [SNP] or diethylenetriamine NONOate [DETA]; 125 to 500 μM) results in noteworthy enhancement in seedling growth in a concentration dependent manner irrespective of salt-stress and differentially affects POD activity in 2-day old seedling cotyledons...
2018: PloS One
https://www.readbyqxmd.com/read/29766351/comparative-whole-genome-re-sequencing-analysis-in-upland-new-rice-for-africa-insights-into-the-breeding-history-and-respective-genome-compositions
#15
Naoki Yamamoto, Richard Garcia, Tomohiro Suzuki, Celymar Angela Solis, Yuichi Tada, Ramaiah Venuprasad, Ajay Kohli
BACKGROUND: Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties...
May 15, 2018: Rice
https://www.readbyqxmd.com/read/29765250/genetic-variants-in-the-exon-region-of-versican-predict-survival-of-patients-with-resected-early-stage-hepatitis-b-virus-associated-hepatocellular-carcinoma
#16
Xiaoguang Liu, Chuangye Han, Xiwen Liao, Long Yu, Guangzhi Zhu, Hao Su, Wei Qin, Sicong Lu, Xinping Ye, Tao Peng
Background: The upregulated expression of versican (VCAN) promotes the proliferation, invasion, and metastasis of various types of human cancer cells, including hepatocellular carcinoma (HCC) cells. Patients and methods: In this study, genetic variants in the exon region of VCAN were genotyped by DNA sequencing. Prognostic values of VCAN exon single nucleotide polymorphisms (SNPs) were assessed by Kaplan-Meier with the log-rank test, and uni- and multivariate Cox proportional hazard regression model...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29763751/integration-of-summary-data-from-gwas-and-eqtl-studies-identified-novel-causal-bmd-genes-with-functional-predictions
#17
Xiang-He Meng, Xiang-Ding Chen, Jonathan Greenbaum, Qin Zeng, Sheng-Lan You, Hong-Mei Xiao, Li-Jun Tan, Hong-Wen Deng
PURPOSE: Osteoporosis is a common global health problem characterized by low bone mineral density (BMD) and increased risk of fracture. Genome-wide association studies (GWAS) have identified >100 genetic loci associated with BMD. However, the functional genes responsible for most associations remain largely unknown. We conducted an innovative summary statistic data-based Mendelian randomization (SMR) analysis to identify novel causal genes associated with BMD and explored their potential functional significance...
May 12, 2018: Bone
https://www.readbyqxmd.com/read/29763720/bap1-loss-is-unusual-in-well-differentiated-papillary-mesothelioma-and-may-predict-development-of-malignant-mesothelioma
#18
Hee Eun Lee, Julian R Molina, William R Sukov, Anja C Roden, Eunhee S Yi
Literature on BRCA1-associated protein 1 (BAP1) expression status in well-differentiated papillary mesothelioma (WDPM) is limited. In the present study, we examined the prevalence of BAP1 loss in WDPM by immunohistochemistry with clinical correlation, along with CDKN2A deletion status by fluorescence in situ hybridization (FISH). Eight patients diagnosed as WDPM were identified from the surgical pathology file. Adenomatoid tumors (n=8) and malignant mesothelioma (MM) (n=39) were included for comparison. BAP1 immunohistochemistry was performed on representative block(s) from each case...
May 12, 2018: Human Pathology
https://www.readbyqxmd.com/read/29761786/association-of-a-four-locus-gene-model-including-il13-il4-fcer1b-and-adrb2-with-the-asthma-predictive-index-and-atopy-in-chinese-han-children
#19
S Bai, L Hua, X Wang, Q Liu, Y Bao
BACKGROUND AND OBJECTIVE: Asthma is a complex and heterogeneous disease. We found that gene-gene interactions among IL13 rs20541, IL4 rs2243250, ADRB2 rs1042713, and FCER1B rs569108 in asthmatic children of Chinese Han nationality. This four-locus set constituted an optimal statistical interaction model. Objective: This study examined associations of the four-gene model consisting of IL13, IL4, FCER1B, and ADRB2 with the Asthma Predictive Index (API) and atopy in Chinese Han children...
May 11, 2018: Journal of Investigational Allergology & Clinical Immunology
https://www.readbyqxmd.com/read/29761124/progranulin-levels-in-blood-in-alzheimer-s-disease-and-mild-cognitive-impairment
#20
Yonatan A Cooper, Daniel Nachun, Deepika Dokuru, Zhongan Yang, Anna M Karydas, Ginette Serrero, Binbin Yue, Adam L Boxer, Bruce L Miller, Giovanni Coppola
Objective: Changes in progranulin ( GRN ) expression have been hypothesized to alter risk for Alzheimer's disease (AD). We investigated the relationship between GRN expression in peripheral blood and clinical diagnosis of AD and mild cognitive impairment (MCI). Methods: Peripheral blood progranulin gene expression was measured, using microarrays from Alzheimer's ( n = 186), MCI ( n = 118), and control ( n = 204) subjects from the University of California San Francisco Memory and Aging Center (UCSF-MAC) and two independent published series (AddNeuroMed and ADNI)...
May 2018: Annals of Clinical and Translational Neurology
keyword
keyword
115174
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"