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Genetics cross validation

Benjamin Stich, Delphine Van Inghelandt
Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy...
2018: Frontiers in Plant Science
Chandrika Bhattacharyya, Partha Pratim Majumder, Bhaswati Pandit
INTRODUCTION: Variability in clinical outcome of tuberculosis infection is dependent, among other factors, on variation in host immunological response to the infection, which is modulated, in part by genetic variations present in the host. We undertook a study to identify host factors associated with such clinical variability. STUDY DESIGN AND METHODS: A comparative study between groups of active TB patients vs. clinically normal household contacts, family members living under the same roof with the patients for a long period of time, was carried out...
March 2018: Tuberculosis
Zhangxia Lyu, Jingru Shao, Min Xue, Qingqing Ye, Bing Chen, Yan Qin, Jianfan Wen
BACKGROUND: Giardia spp. are flagellated protozoan parasites that infect humans and many other vertebrates worldwide. Currently seven species of Giardia are considered valid. RESULTS: Here, we report a new species, Giardia cricetidarum n. sp. in hamsters. Trophozoites of G. cricetidarum n. sp. are pear-shaped with four pairs of flagella and measure on average 14 μm (range 12-18 μm) in length and 10 μm (range 8-12 μm) in width. The trophozoites of the new species are generally larger and stouter than those of most of the other Giardia spp...
March 20, 2018: Parasites & Vectors
Germano Orrù, Mauro Giovanni Carta
Background: Bipolar Disorder (BD), along with depression and schizophrenia, is one of the most serious mental illnesses, and one of the top 20 causes of severe impairment in everyday life. Recent molecular studies, using both traditional approaches and new procedures such as Whole-Genome Sequencing (WGS), have suggested that genetic factors could significantly contribute to the development of BD, with heritability estimates of up to 85%. However, it is assumed that BD is a multigenic and multifactorial illness with environmental factors that strongly contribute to disease development/progression, which means that progress in genetic knowledge of BD might be difficult to interpret in clinical practice...
2018: Clinical Practice and Epidemiology in Mental Health: CP & EMH
François Ancien, Fabrizio Pucci, Maxime Godfroid, Marianne Rooman
The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to loss of protein structure or function. We developed a stability-driven knowledge-based classifier that uses protein structure, artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to predict whether destabilizing or stabilizing mutations are disease-causing...
March 14, 2018: Scientific Reports
Marie C Matrka, Katherine A Cimperman, Sarah R Haas, Geraldine Guasch, Lisa A Ehrman, Ronald R Waclaw, Kakajan Komurov, Adam Lane, Kathryn A Wikenheiser-Brokamp, Susanne I Wells
Esophageal cancer occurs as either squamous cell carcinoma (ESCC) or adenocarcinoma. ESCCs comprise almost 90% of cases worldwide, and recur with a less than 15% five-year survival rate despite available treatments. The identification of new ESCC drivers and therapeutic targets is critical for improving outcomes. Here we report that expression of the human DEK oncogene is strongly upregulated in esophageal SCC based on data in the cancer genome atlas (TCGA). DEK is a chromatin-associated protein with important roles in several nuclear processes including gene transcription, epigenetics, and DNA repair...
March 14, 2018: PLoS Genetics
Amanda B Zheutlin, Adam M Chekroud, Renato Polimanti, Joel Gelernter, Fred W Sabb, Robert M Bilder, Nelson Freimer, Edythe D London, Christina M Hultman, Tyrone D Cannon
Genetic risk variants for schizophrenia have been linked to many related clinical and biological phenotypes with the hopes of delineating how individual variation across thousands of variants corresponds to the clinical and etiologic heterogeneity within schizophrenia. This has primarily been done using risk score profiling, which aggregates effects across all variants into a single predictor. While effective, this method lacks flexibility in certain domains: risk scores cannot capture nonlinear effects and do not employ any variable selection...
March 9, 2018: Schizophrenia Bulletin
Heng Ye, Li Song, Huatao Chen, Babu Valliyodan, Liakat Ali, Tri Vuong, Chengjun Wu, John Orlowski, Blair Buckley, Pengyin Chen, J Grover Shannon, Henry T Nguyen
Natural genetic variations in waterlogging tolerance are controlled by multiple genes mapped as quantitative trait loci (QTL) in major crops, including soybean (Glycine max L.). In this research, two novel QTL associated with waterlogging tolerance were mapped from an elite/exotic soybean cross. The subsequent research was focused on a major QTL (qWT_Gm03) with the tolerant allele from the exotic parent. This QTL was isolated into near-isogenic backgrounds and its effects on waterlogging tolerance were validated in multiple environments...
March 8, 2018: Plant, Cell & Environment
Kamel Mansouri, Chris M Grulke, Richard S Judson, Antony J Williams
The collection of chemical structure information and associated experimental data for quantitative structure-activity/property relationship (QSAR/QSPR) modeling is facilitated by an increasing number of public databases containing large amounts of useful data. However, the performance of QSAR models highly depends on the quality of the data and modeling methodology used. This study aims to develop robust QSAR/QSPR models for chemical properties of environmental interest that can be used for regulatory purposes...
March 8, 2018: Journal of Cheminformatics
Zhaowen Liu, Jie Zhang, Xiaohua Xie, Edmund T Rolls, Jiangzhou Sun, Kai Zhang, Zeyu Jiao, Qunlin Chen, Junying Zhang, Jiang Qiu, Jianfeng Feng
Creative thinking plays a vital role in almost all aspects of human life. However, little is known about the neural and genetic mechanisms underlying creative thinking. Based on a cross-validation based predictive framework, we searched from the whole-brain connectome (34,716 functional connectivities) and whole genome data (309,996 SNPs) in two datasets (all collected by Southwest University, Chongqing) consisting of altogether 236 subjects, for a better understanding of the brain and genetic underpinning of creativity...
March 5, 2018: NeuroImage
Yuxia Zhang, Cui Liu, Jingna Wang, Xingxia Li
To explore genetic pathway cross-talk in neonates with sepsis, an integrated approach was used in this paper. To explore the potential relationships between differently expressed genes between normal uninfected neonates and neonates with sepsis and pathways, genetic profiling and biologic signaling pathway were first integrated. For different pathways, the score was obtained based upon the genetic expression by quantitatively analyzing the pathway cross-talk. The paired pathways with high cross-talk were identified by random forest classification...
March 2018: Experimental Biology and Medicine
Kelly A Mitok, Elyse C Freiberger, Kathryn L Schueler, Mary E Rabaglia, Donald S Stapleton, Nicholas W Kwiecien, Paige A Malec, Alexander S Hebert, Aimee T Broman, Robert T Kennedy, Mark P Keller, Joshua J Coon, Alan D Attie
The mouse is a critical model in diabetes research, but most research in mice has been limited to a small number of mouse strains and limited genetic variation. We used the eight founder strains of the Collaborative Cross (CC) (C57BL/6J (B6), A/J, 129S1/SvImJ (129), NOD/ShiLtJ (NOD), NZO/HILtJ (NZO), PWK/PhJ (PWK), WSB/EiJ (WSB), CAST/EiJ (CAST)) to investigate the genetic dependence of diabetes-related metabolic phenotypes and insulin secretion. We found that strain background is associated with an extraordinary range in body weight, plasma glucose, insulin, and triglycerides, and insulin secretion...
March 1, 2018: Journal of Biological Chemistry
Omnia Gamal El-Dien, Blaise Ratcliffe, Jaroslav Klápště, Ilga Porth, Charles Chen, Yousry A El-Kassaby
The advantages of open-pollinated (OP) family testing over controlled crossing (i.e., structured pedigree) are the potential to screen and rank a large number of parents and offspring with minimal cost and efforts; however, the method produces inflated genetic parameters as the actual sibling relatedness within OP families rarely meets the half-sib relatedness assumption. Here, we demonstrate the unsurpassed utility of OP testing after shifting the analytical mode from pedigree- (ABLUP) to genomic-based (GBLUP) relationship using phenotypic tree height (HT) and wood density (WD) and genotypic (30k SNPs) data for 1126 38-year-old Interior spruce ( Picea glauca (Moench) Voss x P...
2018: Molecular Breeding: New Strategies in Plant Improvement
Junghyun Jung, Go Woon Kim, Woosuk Lee, Changsoo Mok, Sung Hyun Chung, Wonhee Jang
Ample evidence indicates that insulin resistance (IR) is closely related to white adipose tissue (WAT), but the underlying mechanisms of IR pathogenesis are still unclear. Using 352 microarray datasets from seven independent studies, we identified a meta-signature which comprised of 1,413 genes. Our meta-signature was also enriched in overall WAT in in vitro and in vivo IR models. Only 12 core enrichment genes were consistently enriched across all IR models. Among the meta-signature, we identified a drug signature made up of 211 genes with expression levels that were co-regulated by thiazolidinediones and metformin using cross-species analysis...
February 27, 2018: Scientific Reports
Andrew R M Bradbury, Nathan D Trinklein, Holger Thie, Ian C Wilkinson, Atul K Tandon, Stephen Anderson, Catherine L Bladen, Brittany Jones, Shelley Force Aldred, Marco Bestagno, Oscar Burrone, Jennifer Maynard, Fortunato Ferrara, James S Trimmer, Janina Görnemann, Jacob Glanville, Philipp Wolf, Andre Frenzel, Julin Wong, Xin Yu Koh, Hui-Yan Eng, David Lane, Marie-Paule Lefranc, Mike Clark, Stefan Dübel
Monoclonal antibodies are commonly assumed to be monospecific, but anecdotal studies have reported genetic diversity in antibody heavy chain and light chain genes found within individual hybridomas. As the prevalence of such diversity has never been explored, we analyzed 185 random hybridomas, in a large multicenter dataset. The hybridomas analyzed were not biased towards those with cloning difficulties or known to have additional chains. Of the hybridomas we evaluated, 126 (68.1%) contained no additional productive chains, while the remaining 59 (31...
February 27, 2018: MAbs
Dongdong Lin, Jiayu Chen, Nora Perrone-Bizzozero, Juan R Bustillo, Yuhui Du, Vince D Calhoun, Jingyu Liu
BACKGROUND: One of the major challenges in current psychiatric epigenetic studies is the tissue specificity of epigenetic changes since access to brain samples is limited. Peripheral tissues have been studied as surrogates but the knowledge of cross-tissue genetic-epigenetic characteristics remains largely unknown. In this work, we conducted a comprehensive investigation of genetic influence on DNA methylation across brain and peripheral tissues with the aim to characterize cross-tissue genetic-epigenetic effects and their roles in the pathophysiology of psychiatric disorders...
February 26, 2018: Genome Medicine
Paul Harmatz, Chester B Whitley, Raymond Y Wang, Mislen Bauer, Wenjie Song, Christine Haller, Emil Kakkis
BACKGROUND: Drug development for ultra-rare diseases is challenging because small sample sizes and heterogeneous study populations hamper the ability of randomized, placebo-controlled trials with a single primary endpoint to demonstrate valid treatment effects. METHODS: To overcome these challenges, a novel Blind Start design was utilized in a study of vestronidase alfa in mucopolysaccharidosis VII (Sly syndrome), an ultra-rare lysosomal disease, that demonstrates the strengths of this approach in a challenging drug-development setting...
February 12, 2018: Molecular Genetics and Metabolism
Kaio Olímpio Das Graças Dias, Salvador Alejandro Gezan, Claudia Teixeira Guimarães, Alireza Nazarian, Luciano da Costa E Silva, Sidney Netto Parentoni, Paulo Evaristo de Oliveira Guimarães, Carina de Oliveira Anoni, José Maria Villela Pádua, Marcos de Oliveira Pinto, Roberto Willians Noda, Carlos Alexandre Gomes Ribeiro, Jurandir Vieira de Magalhães, Antonio Augusto Franco Garcia, João Cândido de Souza, Lauro José Moreira Guimarães, Maria Marta Pastina
Breeding for drought tolerance is a challenging task that requires costly, extensive, and precise phenotyping. Genomic selection (GS) can be used to maximize selection efficiency and the genetic gains in maize (Zea mays L.) breeding programs for drought tolerance. Here, we evaluated the accuracy of genomic selection (GS) using additive (A) and additive + dominance (AD) models to predict the performance of untested maize single-cross hybrids for drought tolerance in multi-environment trials. Phenotypic data of five drought tolerance traits were measured in 308 hybrids along eight trials under water-stressed (WS) and well-watered (WW) conditions over two years and two locations in Brazil...
February 23, 2018: Heredity
Arne Rosen, Yaser Hasan, William Briggs, Ralf Uptmoor
The development of cauliflower ( Brassica oleracea var. botrytis ) is highly dependent on temperature due to vernalization requirements, which often causes delay and unevenness in maturity during months with warm temperatures. Integrating quantitative genetic analyses with phenology modeling was suggested to accelerate breeding strategies toward wide-adaptation cauliflower. The present study aims at establishing a genome-based model simulating the development of doubled haploid (DH) cauliflower lines to predict time to curd induction of DH lines not used for model parameterization and test hybrids derived from the bi-parental cross...
2018: Frontiers in Plant Science
S Pamela K Shiao, James Grayson, Chong Ho Yu, Brandi Wasek, Teodoro Bottiglieri
For the personalization of polygenic/omics-based health care, the purpose of this study was to examine the gene-environment interactions and predictors of colorectal cancer (CRC) by including five key genes in the one-carbon metabolism pathways. In this proof-of-concept study, we included a total of 54 families and 108 participants, 54 CRC cases and 54 matched family friends representing four major racial ethnic groups in southern California (White, Asian, Hispanics, and Black). We used three phases of data analytics, including exploratory, family-based analyses adjusting for the dependence within the family for sharing genetic heritage, the ensemble method, and generalized regression models for predictive modeling with a machine learning validation procedure to validate the results for enhanced prediction and reproducibility...
February 16, 2018: Journal of Personalized Medicine
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