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Genetics cross validation

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https://www.readbyqxmd.com/read/28540572/characterization-and-mapping-of-dt1-locus-which-co-segregates-with-cctfl1-for-growth-habit-in-pigeonpea
#1
Rachit K Saxena, Jimmy Obala, Andrey Sinjushin, C V Sameer Kumar, K B Saxena, Rajeev K Varshney
We report growth habit profiling following SEM, genetic mapping and QTL analysis. Highlighted CcTFL1 , a candidate for determinacy in pigeonpea, since an Indel marker derived from this gene co-segregated with Dt1 locus. Pigeonpea (Cajanus cajan) is one of the most important legume crops grown in arid and semi-arid regions of the world. It is characterized with few unique features compared with other legume species, such as Lotus, Medicago, and Glycine. One of them is growth habit, an important agronomic trait...
May 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28534096/genomic-prediction-ability-for-yield-related-traits-in-german-winter-barley-elite-material
#2
Patrick Thorwarth, Jutta Ahlemeyer, Anne-Marie Bochard, Kerstin Krumnacker, Hubert Blümel, Eberhard Laubach, Nadine Knöchel, László Cselényi, Frank Ordon, Karl J Schmid
Genomic prediction was evaluated in German winter barley breeding lines. In this material, prediction ability is strongly influenced by population structure and main determinant of prediction ability is the close genetic relatedness of the breeding material. To ensure breeding progress under changing environmental conditions the implementation and evaluation of new breeding methods is of crucial importance. Modern breeding approaches like genomic selection may significantly accelerate breeding progress. We assessed the potential of genomic prediction in a training population of 750 genotypes, consisting of multiple six-rowed winter barley (Hordeum vulgare L...
May 22, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28526731/validated-bayesian-differentiation-of-causative-and-passenger-mutations
#3
Frederick R Cross, Michal Breker, Kristi Lieberman
In many contexts, the problem arises of determining which of many candidate mutations is the most likely to be causative for some phenotype. It is desirable to have a way to evaluate this probability that relies as little as possible on previous knowledge, to avoid bias against discovering new genes or functions. We are isolating mutants with blocked cell cycle progression in Chlamydomonas, and determining mutant genome sequences. Due to the intensity of UV mutagenesis required for efficient mutant collection, the mutants contain multiple mutations altering coding sequence...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28524106/connecting-the-dots-from-an-easy-method-to-computerized-species-determination
#4
Senta Niederegger, Klaus-Peter Döge, Marcus Peter, Tobias Eickhölter, Gita Mall
Differences in growth rate of forensically important dipteran larvae make species determination an essential requisite for an accurate estimation of time since colonization of the body. Interspecific morphological similarities, however, complicate species determination. Muscle attachment site (MAS) patterns on the inside of the cuticula of fly larvae are species specific and grow proportionally with the animal. The patterns can therefore be used for species identification, as well as age estimation in forensically important dipteran larvae...
May 18, 2017: Insects
https://www.readbyqxmd.com/read/28513235/impact-of-interaction-between-cyp1a1-genetic-polymorphisms-and-smoking-on-coronary-artery-disease-in-the-han-of-china
#5
Dao-Di Peng, Wei Xie, Zai-Xin Yu
AIMS: To investigate the association of CYP1A1 genotype and additional gene-smoking interaction with coronary artery disease (CAD) risk based on a Chinese case-control study. METHODS: A total of 1862 participants (1134 men, 728 women) were selected, including 620 CAD patients and 1242 normal controls. Logistic regression was performed to investigate association of CYP1A1 genotype, gene-gene, and gene-smoking interaction with CAD. Generalized multifactor dimensionality reduction (GMDR) was used to screen the best gene-gene and gene-smoking interaction combination, cross-validation consistency, the testing balanced accuracy, and the sign test, to assess if each selected interaction was calculated...
May 17, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28502728/technical-validation-of-a-next-generation-sequencing-assay-for-detecting-clinically-relevant-levels-of-breast-cancer-related-single-nucleotide-variants-and-copy-number-variants-using-simulated-cell-free-dna
#6
Xin Yang, Yuxing Chu, Rui Zhang, Yanxi Han, Lucheng Zhang, Yu Fu, Dan Li, Rongxue Peng, Dongdong Li, Jiansheng Ding, Ziyang Li, Meiru Zhao, Kuo Zhang, Tian Lu, Lang Yi, Qisheng Wu, Guigao Lin, Jiehong Xie, Tao Liu, Ling Yang, Xin Yi, Jinming Li
Next-generation sequencing (NGS) is commonly used in a clinical setting for diagnostic and prognostic testing of genetic mutations to select optimal targeted therapies. Herein, we describe the development of a custom NGS assay for detecting single-nucleotide variants (SNVs) and copy number variations (CNVs) in a panel of 51 genes related to breast cancer. We designed and implemented a validation strategy in accordance with principles and guidelines developed by the Next-Generation Sequencing: Standardization of Clinical Testing work group using artificial, cell-free DNA (cfDNA) with mutant fragments prepared in a simple, rapid, and cost-effective manner...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28500464/global-skin-colour-prediction-from-dna
#7
Susan Walsh, Lakshmi Chaitanya, Krystal Breslin, Charanya Muralidharan, Agnieszka Bronikowska, Ewelina Pospiech, Julia Koller, Leda Kovatsi, Andreas Wollstein, Wojciech Branicki, Fan Liu, Manfred Kayser
Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations...
May 12, 2017: Human Genetics
https://www.readbyqxmd.com/read/28489870/new-gssr-and-est-ssr-markers-reveal-high-genetic-diversity-in-the-invasive-plant-ambrosia-artemisiifolia-l-and-can-be-transferred-to-other-invasive-ambrosia-species
#8
Lucie Meyer, Romain Causse, Fanny Pernin, Romain Scalone, Géraldine Bailly, Bruno Chauvel, Christophe Délye, Valérie Le Corre
Ambrosia artemisiifolia L., (common ragweed), is an annual invasive and highly troublesome plant species originating from North America that has become widespread across Europe. New sets of genomic and expressed sequence tag (EST) based simple sequence repeats (SSRs) markers were developed in this species using three approaches. After validation, 13 genomic SSRs and 13 EST-SSRs were retained and used to characterize the genetic diversity and population genetic structure of Ambrosia artemisiifolia populations from the native (North America) and invasive (Europe) ranges of the species...
2017: PloS One
https://www.readbyqxmd.com/read/28489789/effective-and-extensible-feature-extraction-method-using-genetic-algorithm-based-frequency-domain-feature-search-for-epileptic-eeg-multiclassification
#9
Tingxi Wen, Zhongnan Zhang
In this paper, genetic algorithm-based frequency-domain feature search (GAFDS) method is proposed for the electroencephalogram (EEG) analysis of epilepsy. In this method, frequency-domain features are first searched and then combined with nonlinear features. Subsequently, these features are selected and optimized to classify EEG signals. The extracted features are analyzed experimentally. The features extracted by GAFDS show remarkable independence, and they are superior to the nonlinear features in terms of the ratio of interclass distance and intraclass distance...
May 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28489582/association-between-the-ercc2-asp312asn-polymorphism-and-risk-of-cancer
#10
REVIEW
Feifan Xiao, Jian Pu, Qiongxian Wen, Qin Huang, Qinle Zhang, Birong Huang, Shanshan Huang, Aihua Lan, Yuening Zhang, Jiatong Li, Dong Zhao, Jing Shen, Huayu Wu, Yan He, Hongtao Li, Xiaoli Yang
Cancer is the leading cause of death in economically developed countries and the second leading cause of death in developing countries. The relationship between genetic polymorphisms and the risk of cancers has been widely researched. Excision repair cross-complementing group 2 (ERCC2) gene plays important roles in the nucleotide excision repair pathway. There is contrasting evidence on the association between the ERCC2 Asp312Asn polymorphism and the risk of cancer. We conducted a comprehensive meta-analysis in order to assess the correlation between these factors...
April 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/28484482/investigation-of-the-genetic-diversity-and-quantitative-trait-loci-accounting-for-important-agronomic-and-seed-quality-traits-in-brassica-carinata
#11
Wenshan Zhang, Dandan Hu, Rosy Raman, Shaomin Guo, Zili Wei, Xueqi Shen, Jinling Meng, Harsh Raman, Jun Zou
Brassica carinata (BBCC) is an allotetraploid in Brassicas with unique alleles for agronomic traits and has huge potential as source for biodiesel production. To investigate the genome-wide molecular diversity, population structure and linkage disequilibrium (LD) pattern in this species, we genotyped a panel of 81 accessions of B. carinata with genotyping by sequencing approach DArTseq, generating a total of 54,510 polymorphic markers. Two subpopulations were exhibited in the B. carinata accessions. The average distance of LD decay (r(2) = 0...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28484283/predicting-influenza-antigenicity-from-hemagglutintin-sequence-data-based-on-a-joint-random-forest-method
#12
Yuhua Yao, Xianhong Li, Bo Liao, Li Huang, Pingan He, Fayou Wang, Jiasheng Yang, Hailiang Sun, Yulong Zhao, Jialiang Yang
Timely identification of emerging antigenic variants is critical to influenza vaccine design. The accuracy of a sequence-based antigenic prediction method relies on the choice of amino acids substitution matrices. In this study, we first compared a comprehensive 95 substitution matrices reflecting various amino acids properties in predicting the antigenicity of influenza viruses by a random forest model. We then proposed a novel algorithm called joint random forest regression (JRFR) to jointly consider top substitution matrices...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28478978/interactions-among-variants-in-eicosanoid-genes-increase-risk-of-atherothrombotic-stroke-in-chinese-populations
#13
Xingyang Yi, Jing Lin, Chun Wang, Ruyue Huang, Yingying Liu
BACKGROUND: Eicosanoids are lipid mediators that may play a role in ischemic stroke (IS). However, the association of variants in eicosanoid genes and these interactions with IS risk has not been investigated. The aim of the present study was to investigate the association of 11 variants in eicosanoid genes with IS and to determine whether these gene-gene interactions increase the risk of IS. METHODS: Eleven variants in prostaglandin H synthase-1 (PTGS1), PTGS2, thromboxane A2 synthase (TBXAS1), prostacyclin synthase (PTGIS), and prostaglandin E synthase (PTGES) genes were examined using mass spectrometry method in 297 patients with atherothrombotic stroke and 291 controls...
May 3, 2017: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/28472234/comparison-of-breast-cancer-molecular-features-and-survival-by-african-and-european-ancestry-in-the-cancer-genome-atlas
#14
Dezheng Huo, Hai Hu, Suhn K Rhie, Eric R Gamazon, Andrew D Cherniack, Jianfang Liu, Toshio F Yoshimatsu, Jason J Pitt, Katherine A Hoadley, Melissa Troester, Yuanbin Ru, Tara Lichtenberg, Lori A Sturtz, Carl S Shelley, Christopher C Benz, Gordon B Mills, Peter W Laird, Craig D Shriver, Charles M Perou, Olufunmilayo I Olopade
Importance: African Americans have the highest breast cancer mortality rate. Although racial difference in the distribution of intrinsic subtypes of breast cancer is known, it is unclear if there are other inherent genomic differences that contribute to the survival disparities. Objectives: To investigate racial differences in breast cancer molecular features and survival and to estimate the heritability of breast cancer subtypes. Design, Setting, and Participants: Among a convenience cohort of patients with invasive breast cancer, breast tumor and matched normal tissue sample data (as of September 18, 2015) were obtained from The Cancer Genome Atlas...
May 4, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28471701/the-brain-derived-neurotrophic-factor-val66met-polymorphism-delivery-method-birth-weight-and-night-sleep-duration-as-determinants-of-obesity-in-vietnamese-children-of-primary-school-age
#15
Le Thi Tuyet, Bui Thi Nhung, Duong Thi Anh Dao, Nguyen Thi Hong Hanh, Le Danh Tuyen, Tran Quang Binh, Vu Thi Minh Thuc
BACKGROUND: Obesity is a complex disease that involves both environmental and genetic factors in its pathogenesis. Several studies have identified multiple obesity-associated loci in many populations. However, their contribution to obesity in the Vietnamese population is not fully described, especially in children. The study aimed to investigate the association of obesity with Val66Met polymorphism in brain-derived neurotrophic factor (BDNF) gene, delivery method, birth weight, and lifestyle factors in Vietnamese primary school children...
May 4, 2017: Childhood Obesity
https://www.readbyqxmd.com/read/28469704/development-of-a-core-clostridium-thermocellum-kinetic-metabolic-model-consistent-with-multiple-genetic-perturbations
#16
Satyakam Dash, Ali Khodayari, Jilai Zhou, Evert K Holwerda, Daniel G Olson, Lee R Lynd, Costas D Maranas
BACKGROUND: Clostridium thermocellum is a Gram-positive anaerobe with the ability to hydrolyze and metabolize cellulose into biofuels such as ethanol, making it an attractive candidate for consolidated bioprocessing (CBP). At present, metabolic engineering in C. thermocellum is hindered due to the incomplete description of its metabolic repertoire and regulation within a predictive metabolic model. Genome-scale metabolic (GSM) models augmented with kinetic models of metabolism have been shown to be effective at recapitulating perturbed metabolic phenotypes...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28467816/prediction-of-the-aquatic-toxicity-of-aromatic-compounds-to-tetrahymena-pyriformis-through-support-vector-regression
#17
Qiang Su, Wencong Lu, Dongshu Du, Fuxue Chen, Bing Niu, Kuo-Chen Chou
Toxicity evaluation is an extremely important process during drug development. It is usually initiated by experiments on animals, which is time-consuming and costly. To speed up such a process, a quantitative structure-activity relationship (QSAR) study was performed to develop a computational model for correlating the structures of 581 aromatic compounds with their aquatic toxicity to tetrahymena pyriformis. A set of 68 molecular descriptors derived solely from the structures of the aromatic compounds were calculated based on Gaussian 03, HyperChem 7...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28467728/the-pf4-ppbp-cxcl5-gene-cluster-is-associated-with-periodontitis
#18
A Shusterman, M Munz, G Richter, S Jepsen, W Lieb, B Krone, P Hoffman, M Laudes, J Wellmann, K Berger, T Kocher, S Offenbacher, K Divaris, A Franke, S Schreiber, H Dommisch, E Weiss, A S Schaefer, Y Houri-Haddad, F A Iraqi
Periodontitis is a common dysbiotic inflammatory disease with an estimated heritability of 50%. Due to the limited sample size of available periodontitis cohorts and the underlying trait heterogeneity, genome-wide association studies (GWAS) of chronic periodontitis (CP) have been unsuccessful in discovering susceptibility factors. A strategy that combines agnostic GWAS with a well-powered candidate-gene approach has the potential to discover novel loci. We combined RNA-seq data from gingival tissues with quantitative trait loci (QTLs) that were identified in a F2-cross of mice resistant and susceptible to infection with oral bacterial pathogens...
May 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28464101/genetic-control-of-residual-variance-of-yearling-weight-in-nellore-beef-cattle
#19
L H S Iung, H H R Neves, H A Mulder, R Carvalheiro
There is evidence for genetic variability in residual variance of livestock traits, which offers the potential for selection for increased uniformity of production. Different statistical approaches have been employed to study this topic; however, little is known about the concordance between them. The aim of our study was to investigate the genetic heterogeneity of residual variance on yearling weight (YW; 291.15 ± 46.67) in a Nellore beef cattle population; to compare the results of the statistical approaches, the two-step approach and the double hierarchical generalized linear model (DHGLM); and to evaluate the effectiveness of power transformation to accommodate scale differences...
April 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28464097/live-animal-assessments-of-rump-fat-and-muscle-score-in-angus-cows-and-steers-using-3-dimensional-imaging
#20
M J McPhee, B J Walmsley, B Skinner, B Littler, J P Siddell, L M Cafe, J F Wilkins, V H Oddy, A Alempijevic
The objective of this study was to develop a proof of concept for using off-the-shelf Red Green Blue-Depth (RGB-D) Microsoft Kinect cameras to objectively assess P8 rump fat (P8 fat; mm) and muscle score (MS) traits in Angus cows and steers. Data from low and high muscled cattle (156 cows and 79 steers) were collected at multiple locations and time points. The following steps were required for the 3-dimensional (3D) image data and subsequent machine learning techniques to learn the traits: 1) reduce the high dimensionality of the point cloud data by extracting features from the input signals to produce a compact and representative feature vector, 2) perform global optimization of the signatures using machine learning algorithms and a parallel genetic algorithm, and 3) train a sensor model using regression-supervised learning techniques on the ultrasound P8 fat and the classified learning techniques for the assessed MS for each animal in the data set...
April 2017: Journal of Animal Science
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