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Genetics cross validation

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https://www.readbyqxmd.com/read/27933544/dissection-of-host-susceptibility-to-bacterial-infections-and-its-toxins
#1
Aysar Nashef, Mahmoud Agbaria, Ariel Shusterman, Nicola Ivan Lorè, Alessandra Bragonzi, Ervin Wiess, Yael Houri-Haddad, Fuad A Iraqi
Infection is one of the leading causes of human mortality and morbidity. Exposure to microbial agents is obviously required. However, also non-microbial environmental and host factors play a key role in the onset, development and outcome of infectious disease, resulting in large of clinical variability between individuals in a population infected with the same microbe. Controlled and standardized investigations of the genetics of susceptibility to infectious disease are almost impossible to perform in humans whereas mouse models allow application of powerful genomic techniques to identify and validate causative genes underlying human diseases with complex etiologies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27927935/large-scale-identification-of-patients-with-cerebral-aneurysms-using-natural-language-processing
#2
Victor M Castro, Dmitriy Dligach, Sean Finan, Sheng Yu, Anil Can, Muhammad Abd-El-Barr, Vivian Gainer, Nancy A Shadick, Shawn Murphy, Tianxi Cai, Guergana Savova, Scott T Weiss, Rose Du
OBJECTIVE: To use natural language processing (NLP) in conjunction with the electronic medical record (EMR) to accurately identify patients with cerebral aneurysms and their matched controls. METHODS: ICD-9 and Current Procedural Terminology codes were used to obtain an initial data mart of potential aneurysm patients from the EMR. NLP was then used to train a classification algorithm with .632 bootstrap cross-validation used for correction of overfitting bias. The classification rule was then applied to the full data mart...
December 7, 2016: Neurology
https://www.readbyqxmd.com/read/27926792/the-transcription-factor-pparalpha-is-overexpressed-and-is-associated-with-a-favourable-prognosis-in-idh-wildtype-primary-glioblastoma
#3
H R Haynes, P White, K M Hares, J Redondo, K C Kemp, W G B Singleton, C L Killick-Cole, J R Stevens, K Garadi, S Guglani, A Wilkins, K M Kurian
AIMS: PPARα agonists are in current clinical use as hypolipidaemic agents and show significant antineoplastic effects in human glioblastoma models. To date however, the expression of PPARα in large-scale glioblastoma data sets has not been examined. We aimed to investigate the expression of the transcription factor PPARα in primary glioblastoma, the relationship between PPARα expression and patients' clinicopathological features and other molecular markers associated with gliomagenesis...
December 7, 2016: Histopathology
https://www.readbyqxmd.com/read/27924642/development-of-an-rt-qpcr-assay-for-the-specific-detection-of-a-distinct-genetic-lineage-of-the-infectious-bursal-disease-virus
#4
Gonzalo Tomás, Martín Hernández, Ana Marandino, Claudia Techera, Sofia Grecco, Diego Hernández, Alejandro Banda, Yanina Panzera, Ruben Pérez
The infectious bursal disease virus (IBDV) is a major health threat to the world's poultry industry despite intensive controls including proper biosafety practices and vaccination. IBDV (Avibirnavirus, Birnaviridae) is a non-enveloped virus with a bisegmented double-stranded RNA genome. The virus is traditionally classified into classic, variant and very virulent strains, each with different epidemiological relevance and clinical implications. Recently, a novel worldwide spread genetic lineage was described and denoted as distinct (d) IBDV...
December 7, 2016: Avian Pathology: Journal of the W.V.P.A
https://www.readbyqxmd.com/read/27914629/cytoplasmic-fmr1-interacting-protein-2-is-a-major-genetic-factor-underlying-binge-eating
#5
Stacey L Kirkpatrick, Lisa R Goldberg, Neema Yazdani, R Keith Babbs, Jiayi Wu, Eric R Reed, David F Jenkins, Amanda F Bolgioni, Kelsey I Landaverde, Kimberly P Luttik, Karen S Mitchell, Vivek Kumar, W Evan Johnson, Megan K Mulligan, Pietro Cottone, Camron D Bryant
BACKGROUND: Eating disorders are lethal and heritable; however, the underlying genetic factors are unknown. Binge eating is a highly heritable trait associated with eating disorders that is comorbid with mood and substance use disorders. Therefore, understanding its genetic basis will inform therapeutic development that could improve several comorbid neuropsychiatric conditions. METHODS: We assessed binge eating in closely related C57BL/6 mouse substrains and in an F2 cross to identify quantitative trait loci associated with binge eating...
October 25, 2016: Biological Psychiatry
https://www.readbyqxmd.com/read/27912731/predicting-the-recurrence-of-noncoding-regulatory-mutations-in-cancer
#6
Woojin Yang, Hyoeun Bang, Kiwon Jang, Min Kyung Sung, Jung Kyoon Choi
BACKGROUND: One of the greatest challenges in cancer genomics is to distinguish driver mutations from passenger mutations. Whereas recurrence is a hallmark of driver mutations, it is difficult to observe recurring noncoding mutations owing to a limited amount of whole-genome sequenced samples. Hence, it is required to develop a method to predict potentially recurrent mutations. RESULTS: In this work, we developed a random forest classifier that predicts regulatory mutations that may recur based on the features of the mutations repeatedly appearing in a given cohort...
December 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27908705/a-novel-method-for-in-silico-identification-of-regulatory-snps-in-human-genome
#7
Rong Li, Dexing Zhong, Ruiling Liu, Hongqiang Lv, Xinman Zhang, Jun Liu, Jiuqiang Han
Regulatory single nucleotide polymorphisms (rSNPs), kind of functional noncoding genetic variants, can affect gene expression in a regulatory way, and they are thought to be associated with increased susceptibilities to complex diseases. Here a novel computational approach to identify potential rSNPs is presented. Different from most other rSNPs finding methods which based on hypothesis that SNPs causing large allele-specific changes in transcription factor binding affinities are more likely to play regulatory functions, we use a set of documented experimentally verified rSNPs and nonfunctional background SNPs to train classifiers, so the discriminating features are found...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27903632/genomic-prediction-with-pedigree-and-genotype-%C3%A3-environment-interaction-in-spring-wheat-grown-in-south-and-west-asia-north-africa-and-mexico
#8
Sivakumar Sukumaran, Jose Crossa, Diego Jarquin, Marta Lopes, Mathew P Reynolds
Developing genomic selection (GS) models is an important step in applying GS to accelerate the rate of genetic gain in grain yield in plant breeding. In this study, seven genomic prediction models under two cross-validation scenarios were tested on 287 advanced elite spring wheat lines phenotyped for grain yield (GY), thousand-grain weight (GW), grain number (GN), and thermal time for flowering (TTF) in 18 international environments (year-location combinations) in major wheat producing countries in 2010 and 2011...
November 30, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27902790/accuracy-of-genomic-prediction-in-a-commercial-perennial-ryegrass-breeding-program
#9
Dario Fè, Bilal H Ashraf, Morten G Pedersen, Luc Janss, Stephen Byrne, Niels Roulund, Ingo Lenk, Thomas Didion, Torben Asp, Christian S Jensen, Just Jensen
The implementation of genomic selection (GS) in plant breeding, so far, has been mainly evaluated in crops farmed as homogeneous varieties, and the results have been generally positive. Fewer results are available for species, such as forage grasses, that are grown as heterogenous families (developed from multiparent crosses) in which the control of the genetic variation is far more complex. Here we test the potential for implementing GS in the breeding of perennial ryegrass ( L.) using empirical data from a commercial forage breeding program...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902751/exploration-of-a-polygenic-risk-score-for-alcohol-consumption-a-longitudinal-analysis-from-the-alspac-cohort
#10
Michelle Taylor, Andrew J Simpkin, Philip C Haycock, Frank Dudbridge, Luisa Zuccolo
BACKGROUND: Uncertainty remains about the true extent by which alcohol consumption causes a number of health outcomes. Genetic variants, or combinations of variants built into a polygenic risk score (PGRS), can be used in an instrumental variable framework to assess causality between a phenotype and disease outcome of interest, a method known as Mendelian randomisation (MR). We aimed to identify genetic variants involved in the aetiology of alcohol consumption, and develop a PGRS for alcohol...
2016: PloS One
https://www.readbyqxmd.com/read/27898836/population-genomics-related-to-adaptation-in-elite-oat-germplasm
#11
Kathy Esvelt Klos, Yung-Fen Huang, Wubishet A Bekele, Don E Obert, Ebrahiem Babiker, Aaron D Beattie, Åsmund Bjørnstad, J Michael Bonman, Martin L Carson, Shiaoman Chao, Belaghihalli N Gnanesh, Irene Griffiths, Stephen A Harrison, Catherine J Howarth, Gongshe Hu, Amir Ibrahim, Emir Islamovic, Eric W Jackson, Jean-Luc Jannink, Frederic L Kolb, Michael S McMullen, Jennifer Mitchell Fetch, J Paul Murphy, Herbert W Ohm, Howard W Rines, Brian G Rossnagel, Jessica A Schlueter, Mark E Sorrells, Charlene P Wight, Weikai Yan, Nicholas A Tinker
Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype-phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898835/genomic-prediction-of-barley-hybrid-performance
#12
Norman Philipp, Guozheng Liu, Yusheng Zhao, Sang He, Monika Spiller, Gunther Stiewe, Klaus Pillen, Jochen C Reif, Zuo Li
Hybrid breeding in barley ( L.) offers great opportunities to accelerate the rate of genetic improvement and to boost yield stability. A crucial requirement consists of the efficient selection of superior hybrid combinations. We used comprehensive phenotypic and genomic data from a commercial breeding program with the goal of examining the potential to predict the hybrid performances. The phenotypic data were comprised of replicated grain yield trials for 385 two-way and 408 three-way hybrids evaluated in up to 47 environments...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898829/gapit-version-2-an-enhanced-integrated-tool-for-genomic-association-and-prediction
#13
You Tang, Xiaolei Liu, Jiabo Wang, Meng Li, Qishan Wang, Feng Tian, Zhongbin Su, Yuchun Pan, Di Liu, Alexander E Lipka, Edward S Buckler, Zhiwu Zhang
Most human diseases and agriculturally important traits are complex. Dissecting their genetic architecture requires continued development of innovative and powerful statistical methods. Corresponding advances in computing tools are critical to efficiently use these statistical innovations and to enhance and accelerate biomedical and agricultural research and applications. The genome association and prediction integrated tool (GAPIT) was first released in 2012 and became widely used for genome-wide association studies (GWAS) and genomic prediction...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898821/development-of-a-high-density-linkage-map-and-tagging-leaf-spot-resistance-in-pearl-millet-using-genotyping-by-sequencing-markers
#14
Somashekhar M Punnuri, Jason G Wallace, Joseph E Knoll, Katie E Hyma, Sharon E Mitchell, Edward S Buckler, Rajeev K Varshney, Bharat P Singh
Pearl millet [ (L.) R. Br; also (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines 'Tift 99DB' and 'Tift 454'...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27898759/establishment-and-optimization-of-genomic-selection-to-accelerate-the-domestication-and-improvement-of-intermediate-wheatgrass
#15
Xiaofei Zhang, Ahmad Sallam, Liangliang Gao, Traci Kantarski, Jesse Poland, Lee R DeHaan, Donald L Wyse, James A Anderson
Intermediate wheatgrass (IWG) is a perennial species and has edible and nutritious grain and desirable agronomic traits, including large seed size, high grain yield, and biomass. It also has the potential to provide ecosystem services and an economic return to farmers. However, because of its allohexaploidy and self-incompatibility, developing molecular markers for genetic analysis and molecular breeding has been challenging. In the present study, using genotyping-by-sequencing (GBS) technology, 3436 genome-wide markers discovered in a biparental population with 178 genets, were mapped to 21 linkage groups (LG) corresponding to 21 chromosomes of IWG...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27895389/comparisons-of-dietary-intake-in-japanese-with-non-alcoholic-fatty-liver-disease-and-type-2-diabetes-mellitus
#16
Yukiko Kobayashi, Hina Tatsumi, Mikako Hattori, Hiroki Sugiyama, Sayori Wada, Masashi Kuwahata, Saiyu Tanaka, Kazuyuki Kanemasa, Yoshio Sumida, Yuji Naito, Michiaki Fukui, Yasuhiro Kido
Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease that involves a complex interaction between genetics, diet, and lifestyle, all of which combine to form the NAFLD phenotype. In Japan, medical nutrition therapy for NAFLD has not yet been established, so NAFLD patients are instructed in the dietary modifications used for type 2 diabetes mellitus (T2DM). Because points of difference may exist in the effects of dietary choices on NAFLD and T2DM, the present study aimed to compare and assess the dietary intake of Japanese individuals with NAFLD and T2DM...
November 2016: Journal of Clinical Biochemistry and Nutrition
https://www.readbyqxmd.com/read/27894617/pathway-analysis-based-on-monte-carlo-cross-validation-in-polyarticular-juvenile-idiopathic-arthritis
#17
Shunhua Lin, Yuanji Wang, Shunmei Mu, Junxi Zhang, Fangchang Yuan, Kang Sun
INTRODUCTION: Juvenile idiopathic arthritis (JIA) is a common chronic disease with onset before the 16 years old in a child. Polyarticular JIA has been reported as the main form of JIA in several locations. Until now, understanding of the genetic basis of JIA is incomplete. The purpose of this study was to identify pathway pairs of great potential functional relevance in the progression of polyarticular JIA. MATERIALS AND METHODS: Microarray data of 59 peripheral blood samples from healthy children and 61 samples from polyarticular JIA were transformed to gene expression data...
May 2, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/27894337/intestinal-dysbiosis-is-common-in-systemic-sclerosis-and-associated-with-gastrointestinal-and-extraintestinal-features-of-disease
#18
Kristofer Andréasson, Zaid Alrawi, Anita Persson, Göran Jönsson, Jan Marsal
BACKGROUND: Recent evidence suggests a link between autoimmunity and the intestinal microbial composition in several rheumatic diseases including systemic sclerosis (SSc). The objective of this study was to investigate the prevalence of intestinal dysbiosis in SSc and to characterise patients suffering from this potentially immunomodulatory deviation. METHODS: This study consisted of 98 consecutive patients subject to in-hospital care. Stool samples were analysed for intestinal microbiota composition using a validated genome-based microbiota test (GA-map™ Dysbiosis Test, Genetic Analysis, Oslo, Norway)...
November 29, 2016: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/27890742/serum-uric-acid-and-impaired-cognitive-function-in-community-dwelling-elderly-in-beijing
#19
Shuangling Xiu, Zheng Zheng, Shaochen Guan, Jin Zhang, Jinghong Ma, Piu Chan
The relationship between serum uric acid (sUA) and cognitive function is contradictory. This study assessed the association between sUA and cognitive impairment in 10,039 community-dwelling subjects aged ≥55years living in Beijing, China. Participants underwent determination of sUA and an evaluation of cognitive function using the scholarship-adjusted Mini-Mental State Examination (MMSE): MMSE ≤17 for illiterates; MMSE≤20 for primary school graduates (≥6years of education); and MMSE≤24 for junior school graduates or above (≥9years of education)...
November 24, 2016: Neuroscience Letters
https://www.readbyqxmd.com/read/27890367/evaluation-of-interleukin-8%C3%A2-2767-a-t-polymorphism-in-visceral-leishmaniasis
#20
Alireza Ahmadi, Mehrdad Hajilooi, Ghasem Solgi, Mohammad Abasi, Ahad Bazmani, Alireza Khalilian, Mohammad Matini, Khosro Sardarian
OBJECTIVE: To evaluated the relationship between the genetic variations at IL-8 +2767 position with VL pathogenesis among Iranian patients. METHODS: Three groups including patients with VL clinical presentation and leishmania seropositive (n = 124), patients seropositive but without clinical presentation (n = 82) and healthy controls (n = 63) were selected to conduct this cross-sectional study. Polymorphism at +2767 position of IL-8 was investigated using PCR-RFLP techniques...
November 2016: Asian Pacific Journal of Tropical Medicine
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