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https://www.readbyqxmd.com/read/28936114/practical-application-of-genomic-selection-in-a-doubled-haploid-winter-wheat-breeding-program
#1
Jiayin Song, Brett F Carver, Carol Powers, Liuling Yan, Jaroslav Klápště, Yousry A El-Kassaby, Charles Chen
Crop improvement is a long-term, expensive institutional endeavor. Genomic selection (GS), which uses single nucleotide polymorphism (SNP) information to estimate genomic breeding values, has proven efficient to increasing genetic gain by accelerating the breeding process in animal breeding programs. As for crop improvement, with few exceptions, GS applicability remains in the evaluation of algorithm performance. In this study, we examined factors related to GS applicability in line development stage for grain yield using a hard red winter wheat (Triticum aestivum L...
2017: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/28936065/high-frequency-of-depressive-symptoms-among-adults-with-epilepsy-results-from-a-hospital-based-study
#2
Syam C Chandrasekharan, Vikas Menon, Vaibhav Wadwekar, Pradeep Pankajakshan Nair
CONTEXT: Assessment of comorbid burden of depression and associated factors among adult people living with epilepsy (PWE) has the potential to inform clinical evaluation and management to improve outcomes. AIM: The aim of this study is to determine frequency of depressive symptoms and factors associated with it among PWE attending a tertiary care hospital. SETTING AND DESIGN: This was a cross-sectional observational study conducted in the outpatient clinic of a tertiary care center...
August 2017: Journal of Neurosciences in Rural Practice
https://www.readbyqxmd.com/read/28930629/large-scale-replication-study-identified-multiple-independent-snps-in-ret-synergistically-associated-with-hirschsprung-disease-in-southern-chinese-population
#3
Yan Zhang, Qiuming He, Ruizhong Zhang, Hong Zhang, Wei Zhong, Huimin Xia
Hischsprung disease (HSCR) is an intestinal disorder with strong genetic components. RET was considered as the strongest contributor. Multiple single nucleotide polymorphisms (SNP) were demonstrated as associated with HSCR in different populations. However, whether the associations of reported SNPs derived from one causal variants or congregations of multiple variants were still not clear. In this study, we successfully genotyped 16 SNPs in RET with a largest case-control study to date, totaling 1470 HSCR and 1473 control subjects in South Chinese population...
September 20, 2017: Aging
https://www.readbyqxmd.com/read/28926725/association-between-x-ray-repair-cross-complementing-group-1-xrcc1-arg399gln-polymorphism-and-endometriosis-a-systematic-review-and-meta-analysis
#4
Mo-Qi Lv, Jin Wang, Xiao-Qing Yu, Hui-Hui Hong, Wen-Juan Ren, Pang Ge, Dang-Xia Zhou
OBJECTIVE(S): X-ray repair cross-complementing group 1(XRCC1) gene is one of the DNA repair pathway genes playing a vital role in endometriosis risk. Various studies have explored the association between them, however, the results remained inconsistent. So to confirm the association between XRCC1 Arg399Gln polymorphism and the risk of endometriosis, a meta-analysis was conducted. STUDY DESIGN: PubMed, Web of Science, Science Director, Cochrane Library, Google Scholar, China National Knowledge Infrastructure (CNKI) and Wanfang Data databases were searched to identify the all relevant studies before Sep...
September 14, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28912111/crispr-cas9-mediated-g4946e-substitution-in-the-ryanodine-receptor-of-spodoptera-exigua-confers-high-levels-of-resistance-to-diamide-insecticides
#5
Yayun Zuo, Hui Wang, Yanjun Xu, Jianlei Huang, Shuwen Wu, Yidong Wu, Yihua Yang
Diamide insecticides selectively activate insect ryanodine receptors (RyRs), inducing uncontrolled release of calcium ions, and causing muscle contraction, paralysis and eventually death. The RyR(G4946E) substitution associated with diamide resistance has been identified in three lepidopteran pests, Plutella xylostella, Tuta absoluta and Chilo suppressalis. Recently, the T. absoluta RyR(G4946V) mutation was knocked into the model insect Drosophila melanogaster by CRISPR/Cas9 mediated genome editing and provided in vivo functional confirmation for its role in diamide resistance...
September 12, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28900291/assessing-the-expected-response-to-genomic-selection-of-individuals-and-families-in-eucalyptus-breeding-with-an-additive-dominant-model
#6
R T Resende, M D V Resende, F F Silva, C F Azevedo, E K Takahashi, O B Silva-Junior, D Grattapaglia
We report a genomic selection (GS) study of growth and wood quality traits in an outbred F2 hybrid Eucalyptus population (n=768) using high-density single-nucleotide polymorphism (SNP) genotyping. Going beyond previous reports in forest trees, models were developed for different selection targets, namely, families, individuals within families and individuals across the entire population using a genomic model including dominance. To provide a more breeder-intelligible assessment of the performance of GS we calculated the expected response as the percentage gain over the population average expected genetic value (EGV) for different proportions of genomically selected individuals, using a rigorous cross-validation (CV) scheme that removed relatedness between training and validation sets...
October 2017: Heredity
https://www.readbyqxmd.com/read/28884379/genetic-interaction-of-purinergic-p2x7-receptor-and-er-%C3%AE-polymorphisms-in-susceptibility-to-osteoporosis-in-chinese-postmenopausal-women
#7
Hui Wang, Chengxin Gong, Xingzi Liu, Shenqiang Rao, Tao Li, Luling He, Yijun Nie, Shuo Wang, Peipei Zhong, Yansong Xue, Jihong Wang, Jiani Zhao, Yuru Zhou, Lu Ding, Yunming Tu, Yuping Yang, Chaopeng Xiong, Shangdong Liang, Hong Xu
Osteoporosis (OP) is an increasing public health problem worldwide. Genetic factors are considered to be major contributors to the pathogenesis of OP. The aim of this study was to investigate the association of the purinergic P2X7 receptor (P2X7R) and estrogen receptor-α (ER-α) genes with OP risk, and the effect of the possible interaction between the two genes on predisposition to OP in Chinese postmenopausal women. A total of 596 subjects, including 350 OP patients and 246 controls, were recruited in this case-control study...
September 7, 2017: Journal of Bone and Mineral Metabolism
https://www.readbyqxmd.com/read/28880457/development-of-quality-metrics-for-ambulatory-care-in-pediatric-patients-with-tetralogy-of-fallot
#8
Juan Villafane, Thomas C Edwards, Karim A Diab, Gary M Satou, Elizabeth Saarel, Wyman W Lai, Gerald A Serwer, Peter P Karpawich, Russell Cross, Russell Schiff, Devyani Chowdhury, Thomas J Hougen
OBJECTIVE: The objective of this study was to develop quality metrics (QMs) relating to the ambulatory care of children after complete repair of tetralogy of Fallot (TOF). DESIGN: A workgroup team (WT) of pediatric cardiologists with expertise in all aspects of ambulatory cardiac management was formed at the request of the American College of Cardiology (ACC) and the Adult Congenital and Pediatric Cardiology Council (ACPC), to review published guidelines and consensus data relating to the ambulatory care of repaired TOF patients under the age of 18 years...
September 7, 2017: Congenital Heart Disease
https://www.readbyqxmd.com/read/28864187/quantum-dot-nanoprobes-and-aotf-based-cross-talk-eliminated-six-color-imaging-of-biomolecules-in-cellular-system
#9
Solji Park, Parthasarathy Arumugam, Baskaran Purushothaman, Sung-Yon Kim, Dal-Hee Min, Noo Li Jeon, Joon Myong Song
Primary cell cultures mimic the physiology and genetic makeup of in-vivo tissue of origin, nonetheless, a complication in the derivation and propagation of primary cell culture limits its use in biological research. However, in-vitro models using primary cells might be a complement model to mimic in vivo response. But, conventional techniques such as western blot and PCR employed to study the expression and activation of proteins requires a large number of cells, hence repeated establishment and maintenance of primary culture are unavoidable...
September 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28851378/in-silico-prediction-of-novel-therapeutic-targets-using-gene-disease-association-data
#10
Enrico Ferrero, Ian Dunham, Philippe Sanseau
BACKGROUND: Target identification and validation is a pressing challenge in the pharmaceutical industry, with many of the programmes that fail for efficacy reasons showing poor association between the drug target and the disease. Computational prediction of successful targets could have a considerable impact on attrition rates in the drug discovery pipeline by significantly reducing the initial search space. Here, we explore whether gene-disease association data from the Open Targets platform is sufficient to predict therapeutic targets that are actively being pursued by pharmaceutical companies or are already on the market...
August 29, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28851283/performance-of-risk-prediction-for-inflammatory-bowel-disease-based-on-genotyping-platform-and-genomic-risk-score-method
#11
Guo-Bo Chen, Sang Hong Lee, Grant W Montgomery, Naomi R Wray, Peter M Visscher, Richard B Gearry, Ian C Lawrance, Jane M Andrews, Peter Bampton, Gillian Mahy, Sally Bell, Alissa Walsh, Susan Connor, Miles Sparrow, Lisa M Bowdler, Lisa A Simms, Krupa Krishnaprasad, Graham L Radford-Smith, Gerhard Moser
BACKGROUND: Predicting risk of disease from genotypes is being increasingly proposed for a variety of diagnostic and prognostic purposes. Genome-wide association studies (GWAS) have identified a large number of genome-wide significant susceptibility loci for Crohn's disease (CD) and ulcerative colitis (UC), two subtypes of inflammatory bowel disease (IBD). Recent studies have demonstrated that including only loci that are significantly associated with disease in the prediction model has low predictive power and that power can substantially be improved using a polygenic approach...
August 29, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28845923/clinical-rating-scale-for-pantothenate-kinase-associated-neurodegeneration-a-pilot-study
#12
Alejandra Darling, Cristina Tello, María Josep Martí, Cristina Garrido, Sergio Aguilera-Albesa, Miguel Tomás Vila, Itziar Gastón, Marcos Madruga, Luis González Gutiérrez, Julio Ramos Lizana, Montserrat Pujol, Tania Gavilán Iglesias, Kylee Tustin, Jean Pierre Lin, Giovanna Zorzi, Nardo Nardocci, Loreto Martorell, Gustavo Lorenzo Sanz, Fuencisla Gutiérrez, Pedro J García, Lidia Vela, Carlos Hernández Lahoz, Juan Darío Ortigoza Escobar, Laura Martí Sánchez, Fradique Moreira, Miguel Coelho, Leonor Correia Guedes, Ana Castro Caldas, Joaquim Ferreira, Paula Pires, Cristina Costa, Paulo Rego, Marina Magalhães, María Stamelou, Daniel Cuadras Pallejà, Carmen Rodríguez-Blazquez, Pablo Martínez-Martín, Vincenzo Lupo, Leonidas Stefanis, Roser Pons, Carmen Espinós, Teresa Temudo, Belén Pérez Dueñas
BACKGROUND: Pantothenate kinase-associated neurodegeneration is a progressive neurological disorder occurring in both childhood and adulthood. The objective of this study was to design and pilot-test a disease-specific clinical rating scale for the assessment of patients with pantothenate kinase-associated neurodegeneration. METHODS: In this international cross-sectional study, patients were examined at the referral centers following a standardized protocol. The motor examination was filmed, allowing 3 independent specialists in movement disorders to analyze 28 patients for interrater reliability assessment...
August 28, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28845069/highly-polymorphic-microsatellite-markers-for-the-assessment-of-male-reproductive-skew-and-genetic-variation-in-critically-endangered-crested-macaques-macaca-nigra
#13
Antje Engelhardt, Laura Muniz, Dyah Perwitasari-Farajallah, Anja Widdig
Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques...
2017: International Journal of Primatology
https://www.readbyqxmd.com/read/28833716/genomic-estimation-of-additive-and-dominance-effects-and-impact-of-accounting-for-dominance-on-accuracy-of-genomic-evaluation-in-sheep-populations
#14
N Moghaddar, J H J van der Werf
The objectives of this study were to estimate the additive and dominance variance component of several weight and ultrasound scanned body composition traits in purebred and combined cross-bred sheep populations based on single nucleotide polymorphism (SNP) marker genotypes and then to investigate the effect of fitting additive and dominance effects on accuracy of genomic evaluation. Additive and dominance variance components were estimated in a mixed model equation based on "average information restricted maximum likelihood" using additive and dominance (co)variances between animals calculated from 48,599 SNP marker genotypes...
August 17, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28831069/theoretical-studies-of-intracellular-concentration-of-micro-organisms-metabolites
#15
Hai-Feng Yang, Xiao-Nan Zhang, Yan Li, Yong-Hong Zhang, Qin Xu, Dong-Qing Wei
With the rapid growth of micro-organism metabolic networks, acquiring the intracellular concentration of microorganisms' metabolites accurately in large-batch is critical to the development of metabolic engineering and synthetic biology. Complementary to the experimental methods, computational methods were used as effective assessing tools for the studies of intracellular concentrations of metabolites. In this study, the dataset of 130 metabolites from E. coli and S. cerevisiae with available experimental concentrations were utilized to develop a SVM model of the negative logarithm of the concentration (-logC)...
August 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28827289/mip-map-high-throughput-mapping-of-caenorhabditis-elegans-temperature-sensitive-mutants-via-molecular-inversion-probes
#16
Calvin A Mok, Vinci Au, Owen A Thompson, Mark L Edgley, Louis Gevirtzman, John Yochem, Joshua Lowry, Nadin Memar, Matthew R Wallenfang, Dominique Rasoloson, Bruce Bowerman, Ralf Schnabel, Geraldine Seydoux, Donald G Moerman, Robert H Waterston
Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS)...
August 21, 2017: Genetics
https://www.readbyqxmd.com/read/28819827/interaction-between-selp-genetic-polymorphisms-with-inflammatory-cytokine-interleukin-6-il-6-gene-variants-on-cardiovascular-disease-in-chinese-han-population
#17
Lu Kou, Ning Yang, Bo Dong, Yang Li, Jingyu Yang, Qin Qin
The aim of the study is to investigate the impact of SELP and IL-6 genetic single-nucleotide polymorphisms (SNPs) and its gene-gene interaction on cardiovascular disease (CVD) risk based on Chinese population. A total of 1082 subjects (519 males, 563 females), with a mean age of 53.9 ± 13.1 years, were selected, including 540 CVD patients and 542 normal control participants. Logistic regression model was used to examine the association between six SNPs and CVD risk. Odds ratio (OR) and 95% confident interval (95% CI) were calculated...
August 18, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28814505/the-molecular-architecture-of-the-yeast-spindle-pole-body-core-determined-by-bayesian-integrative-modeling
#18
Shruthi Viswanath, Massimiliano Bonomi, Seung Joong Kim, Vadim A Klenchin, Keenan C Taylor, King C Yabut, Neil T Umbreit, Heather A Van Epps, Janet Meehl, Michele H Jones, Daniel Russel, Javier A Velazquez-Muriel, Mark Winey, Ivan Rayment, Trisha N Davis, Andrej Sali, Eric G Muller
Microtubule organizing centers (MTOCs) form, anchor and stabilize the polarized network of microtubules in a cell. The central MTOC is the centrosome that duplicates during the cell cycle and during mitosis assembles a bipolar spindle to capture and segregate sister chromatids. Yet, despite their importance in cell biology, the physical structure of MTOCs is poorly understood. Here we determine the molecular architecture of the core of the yeast spindle pole body (SPB) by Bayesian integrative structure modeling based on in vivo FRET, small-angle X-ray scattering (SAXS), X-ray crystallography, electron microscopy and two-hybrid analysis...
August 16, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28813480/paleogenetic-study-on-the-17th-century-korean-mummy-with-atherosclerotic-cardiovascular-disease
#19
Dong Hoon Shin, Chang Seok Oh, Jong Ha Hong, Yusu Kim, Soong Deok Lee, Eunju Lee
While atherosclerotic cardiovascular disease (ASCVD) is known to be common among modern people exposed to various risk factors, recent paleopathological studies have shown that it affected ancient populations much more frequently than expected. In 2010, we investigated a 17th century Korean female mummy with presumptive ASCVD signs. Although the resulting report was a rare and invaluable conjecture on the disease status of an ancient East Asian population, the diagnosis had been based only on anatomical and radiological techniques, and so could not confirm the existence of ASCVD in the mummy...
2017: PloS One
https://www.readbyqxmd.com/read/28809947/high-density-genetic-linkage-map-construction-by-f2-populations-and-qtl-analysis-of-early-maturity-traits-in-upland-cotton-gossypium-hirsutum-l
#20
Libei Li, Shuqi Zhao, Junji Su, Shuli Fan, Chaoyou Pang, Hengling Wei, Hantao Wang, Lijiao Gu, Chi Zhang, Guoyuan Liu, Dingwei Yu, Qibao Liu, Xianlong Zhang, Shuxun Yu
Due to China's rapidly increasing population, the total arable land area has dramatically decreased; as a consequence, the competition for farming land allocated for grain and cotton production has become fierce. Therefore, to overcome the existing contradiction between cotton grain and fiber production and the limited farming land, development of early-maturing cultivars is necessary. In this research, a high-density linkage map of upland cotton was constructed using genotyping by sequencing (GBS) to discover single nucleotide polymorphism (SNP) markers associated with early maturity in 170 F2 individuals derived from a cross between LU28 and ZHONG213...
2017: PloS One
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