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Genomic selection

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https://www.readbyqxmd.com/read/28738459/-gene-gene-interaction-on-central-obesity-in-school-aged-children-in-china
#1
L W Fu, M X Zhang, L J Wu, L W Gao, J Mi
Objective: To investigate possible effect of 6 obesity-associated SNPs in contribution to central obesity and examine whether there is an interaction in the 6 SNPs in the cause of central obesity in school-aged children in China. Methods: A total of 3 502 school-aged children who were included in Beijing Child and Adolescent Metabolic Syndrome (BCAMS) Study were selected, and based on the age and sex specific waist circumference (WC) standards in the BCAMS study, 1 196 central obese cases and 2 306 controls were identified...
July 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28738208/plastid-transformation-and-its-application-in-metabolic-engineering
#2
REVIEW
Paulina Fuentes, Tegan Armarego-Marriott, Ralph Bock
Metabolic pathway engineering by transgene expression from the plastid (chloroplast) genome offers significant attractions, including straightforward multigene engineering by pathway expression from operons, high transgene expression levels, and increased transgene containment due to maternal inheritance of plastids in most crops. In addition, it provides direct access to the large and diverse metabolite pools in chloroplasts and non-green plastid types. Here, we review recent progress with extending the toolbox for plastid engineering and highlight selected applications in the area of metabolic engineering, including the combined engineering of nuclear and plastid genomes for the production of artemisinic acid, the direct harness of chloroplast reducing power for the synthesis of dhurrin and the use of an edible host for the production of astaxanthin...
July 21, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28737761/glutamate-receptor-like-channels-are-essential-for-chemotaxis-and-reproduction-in-mosses
#3
Carlos Ortiz-Ramírez, Erwan Michard, Alexander A Simon, Daniel S C Damineli, Marcela Hernández-Coronado, Jörg D Becker, José A Feijó
Glutamate receptors are well characterized channels that mediate cell-to-cell communication during neurotransmission in animals. Nevertheless, information regarding their functional role in organisms without nervous systems is still limited. In plants, Glutamate Receptor-like (GLR) genes have been implicated in defence against pathogens, reproduction, control of stomata aperture and light signal transduction(1-5). However, the numerous GLR genes present in angiosperm genomes (20 to 70)(6) has prevented the observation of strong phenotypes in loss-of-function mutants...
July 24, 2017: Nature
https://www.readbyqxmd.com/read/28737288/linkage-disequilibrium-among-commonly-genotyped-snp-variants-detected-from-bull-sequence
#4
W M Snelling, L A Kuehn, B N Keel, R M Thallman, G L Bennett
Genomic prediction utilizing causal variants could increase selection accuracy above that achieved with SNPs genotyped by currently available arrays used for genomic selection. A number of variants detected from sequencing influential sires are likely to be causal, but noticeable improvements in prediction accuracy using imputed sequence variant genotypes have not been reported. Improvement in accuracy of predicted breeding values may be limited by the accuracy of imputed sequence variants. Using genotypes of SNPs on a high-density array and non-synonymous SNPs detected in sequence from influential sires of a multibreed population, results of this examination suggest that linkage disequilibrium between non-synonymous and array SNPs may be insufficient for accurate imputation from the array to sequence...
July 24, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28737212/a-genome-wide-association-study-for-equine-recurrent-airway-obstruction-in-european-warmblood-horses-reveals-a-suggestive-new-quantitative-trait-locus-on-chromosome-13
#5
D Schnider, S Rieder, T Leeb, V Gerber, M Neuditschko
Recurrent airway obstruction (RAO), also known as heaves, is an asthma-like respiratory disease. Its development is strongly influenced by environmental risk factors such as sensitization and exposure to moldy hay, straw bedding and stabling indoors. A hereditary component has been documented in previous studies; however, so far no causative genetic variant that influences the risk of developing RAO has been identified. In this study, we revised an existing dataset and selected 384 horses for genotyping on the Affymetrix high-density equine SNP array...
July 24, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28736898/identification-of-positive-selection-signatures-in-pigs-by-comparing-linkage-disequilibrium-variances
#6
X Li, S Yang, K Dong, Z Tang, K Li, B Fan, Z Wang, B Liu
Selection affects the patterns of linkage disequilibrium (LD) around the site of a beneficial allele with an increase in LD among the hitchhiking alleles. Comparing the differences in regional LD between pig populations could help to identify putative genomic regions with potential adaptations for economic traits. In this study, using Illumina Porcine SNP60K BeadChip genotyping data from 207 Chinese indigenous, 117 South American village and 408 Large White pigs, we estimated the variation of genome-wide LD between populations using the varld program...
July 23, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28736570/genome-wide-identification-and-functional-analysis-of-the-calcineurin-b-like-protein-and-calcineurin-b-like-protein-interacting-protein-kinase-gene-families-in-turnip-brassica-rapa-var-rapa
#7
Xin Yin, Qiuli Wang, Qian Chen, Nan Xiang, Yunqiang Yang, Yongping Yang
The calcineurin B-like protein (CBL)-CBL-interacting protein kinase (CIPK) complex has been identified as a primary component in calcium sensors that perceives various stress signals. Turnip (Brassica rapa var. rapa) has been widely cultivated in the Qinghai-Tibet Plateau for a century as a food crop of worldwide economic significance. These CBL-CIPK complexes have been demonstrated to play crucial roles in plant response to various environmental stresses. However, no report is available on the genome-wide characterization of these two gene families in turnip...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28736510/a-genomic-perspective-on-the-generation-and-maintenance-of-genetic-diversity-in-herbivorous-insects
#8
Andrew D Gloss, Simon C Groen, Noah K Whiteman
Understanding the processes that generate and maintain genetic variation within populations is a central goal in evolutionary biology. Theory predicts that some of this variation is maintained as a consequence of adapting to variable habitats. Studies in herbivorous insects have played a key role in confirming this prediction. Here, we highlight theoretical and conceptual models for the maintenance of genetic diversity in herbivorous insects, empirical genomic studies testing these models, and pressing questions within the realm of evolutionary and functional genomic studies...
November 2016: Annual Review of Ecology, Evolution, and Systematics
https://www.readbyqxmd.com/read/28736437/dissecting-evolution-and-disease-using-comparative-vertebrate-genomics
#9
REVIEW
Jennifer R S Meadows, Kerstin Lindblad-Toh
With the generation of more than 100 sequenced vertebrate genomes in less than 25 years, the key question arises of how these resources can be used to inform new or ongoing projects. In the past, this diverse collection of sequences from human as well as model and non-model organisms has been used to annotate the human genome and to increase the understanding of human disease. In the future, comparative vertebrate genomics in conjunction with additional genomic resources will yield insights into the processes of genome function, evolution, speciation, selection and adaptation, as well as the quantification of species diversity...
July 24, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28735781/the-future-of-fracture-risk-assessment-in-the-management-of-osteoporosis
#10
Sanford Baim
There have been many advances in the field of osteoporosis that add to a greater understanding of skeletal integrity and the adverse effects menopause and aging have on bone. The World Health Organization, the International Osteoporosis Foundation, and numerous additional governmental and privately sponsored organizations, societies, and their respective task forces have provided guidance for the use of appropriate fracture assessment methodologies and fracture risk assessment tools, and for the prevention and management of osteoporosis...
July 20, 2017: Journal of Clinical Densitometry
https://www.readbyqxmd.com/read/28735487/targeted-next-generation-sequencing-of-acute-leukemia
#11
Eric Konnick, Christina M Lockwood, David Wu
Mutation profiling of acute leukemias is a valuable tool for identifying genetic mutations with prognostic, predictive, therapeutic, and diagnostic utility. Technological advances, such as massively parallel sequencing, have allowed laboratories to assess for variation across dozens or hundreds of genes simultaneously with relatively low cost per target.Here, we describe a procedure for designing and using a TruSeq Custom Amplicon assay targeting genes involved in acute leukemias. This method is a fully customizable, amplicon-based assay for targeted resequencing, allowing interrogation of selected genomic regions of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735482/design-and-application-of-multiplex-pcr-seq-for-the-detection-of-somatic-mutations-associated-with-myeloid-malignancies
#12
Naomi Park, George Vassiliou
Targeted sequencing, in which only a selected set of genomic loci are sequenced, enables a much higher coverage of each target than what is obtained using whole genome or exome sequencing. Multiplex PCR offers a simple and affordable technique for specific capture of target regions and can be easily adapted to generate next-generation sequencing (NGS)-ready amplicons. Here we describe a multiplex PCR (MxPCR) approach for capturing 13 leukemia-associated mutation hotspots followed by MiSeq sequencing that enables robust detection of mutations with a variant allele fraction (VAF) as low as 0...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735109/design-and-rationale-for-a-real-world-observational-cohort-of-patients-with-nonalcoholic-fatty-liver-disease-the-target-nash-study
#13
A Sidney Barritt, Norman Gitlin, Samuel Klein, Anna S Lok, Rohit Loomba, Laura Malahias, Margaret Powell, Miriam B Vos, L Michael Weiss, Kenneth Cusi, Brent A Neuschwander-Tetri, Arun Sanyal
Nonalcoholic fatty liver disease (NAFLD) is highly prevalent and can lead to cirrhosis, hepatocellular carcinoma, and end-stage liver disease. NAFLD comprises the spectrum from simple steatosis (nonalcoholic fatty liver, NAFL), to steatosis with inflammation (nonalcoholic steatohepatitis, NASH). Current primary therapy recommended for NAFLD is weight loss induced by lifestyle modification. The difficulty in achieving this has led to robust pharmacological therapy development. While new drugs may show efficacy in selected phase II/III clinical trial populations, their real-world effectiveness is unknown...
July 19, 2017: Contemporary Clinical Trials
https://www.readbyqxmd.com/read/28734047/preselection-of-recombinant-gene-integration-sites-enabling-high-transcription-rates-in-cho-cells-using-alternate-start-codons-and-recombinase-mediated-cassette-exchange
#14
Martina Baumann, Elisabeth Gludovacz, Natalie Sealover, Scott Bahr, Henry George, Nan Lin, Kevin Kayser, Nicole Borth
Site-specific Recombinase Mediated Cassette Exchange (RMCE) enables the transfer of the gene of interest (GOI) into pre-selected genomic locations with defined expression properties. For the generation of recombinant production cell lines this has the advantage that screening for high transcription rates at the genome integration site would be required only once, with the possibility to reuse the selected site for new products. Here we describe a strategy that aims at the selection of transcriptionally active genome integration sites in Chinese Hamster Ovary (CHO) cells by using alternate start codons in the surface reporter protein CD4, in combination with FACS sorting for high expressers...
July 22, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28733840/identification-of-a%C3%A2-rare-coch-mutation-by-whole-exome-sequencing-implications-for-personalized-therapeutic-rehabilitation-in-an-austrian-family-with-non-syndromic-autosomal-dominant-late-onset-hearing-loss
#15
Thomas Parzefall, Alexandra Frohne, Martin Koenighofer, Andreas Kirchnawy, Berthold Streubel, Christian Schoefer, Wolfgang Gstoettner, Klemens Frei, Trevor Lucas
BACKGROUND: Non-syndromic autosomal dominant hearing impairment is characteristically postlingual in onset. Genetic diagnostics are essential for genetic counselling, disease prognosis and understanding of the molecular mechanisms of disease. To date, 36 causative genes have been identified, many in only individual families. Gene selection for genetic screening by traditional methods and genetic diagnosis in autosomal dominant patients has therefore been fraught with difficulty. Whole-exome sequencing provides a powerful tool to analyze all protein-coding genomic regions in parallel, thus allowing the comprehensive screening of all known genes and associated alterations...
July 21, 2017: Wiener Klinische Wochenschrift
https://www.readbyqxmd.com/read/28733817/enriching-an-intraspecific-genetic-map-and-identifying-qtl-for-fiber-quality-and-yield-component-traits-across-multiple-environments-in-upland-cotton-gossypium-hirsutum-l
#16
Xueying Liu, Zhonghua Teng, Jinxia Wang, Tiantian Wu, Zhiqin Zhang, Xianping Deng, Xiaomei Fang, Zhaoyun Tan, Iftikhar Ali, Dexin Liu, Jian Zhang, Dajun Liu, Fang Liu, Zhengsheng Zhang
Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35 × Yumian 1) recombinant inbred line (RIL) population...
July 21, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28733441/molecular-screening-for-cancer-treatment-optimization-moscato-01-in-pediatric-patients-a-single-institutional-prospective-molecular-stratification-trial
#17
Anne Catherine Harttrampf, Ludovic Lacroix, Marc Deloger, Frederic Deschamps, Stéphanie Puget, Nathalie Auger, Philippe Vielh, Pascale Varlet, Zsofia Balogh, Samuel Abbou, Adrien Allorant, Dominique Valteau-Couanet, Sabine Sarnacki, Louise Galmiche, Guillaume Meurice, Véronique Minard-Colin, Jacques Grill, Laurence Brugières, Christelle Dufour, Nathalie Gaspar, Stefan Michiels, Gilles Vassal, Jean-Charles Soria, Birgit Geoerger
This single institutional feasibility study prospectively characterized genomic alterations in recurrent or refractory solid tumors of pediatric patients in order to select a targeted therapy.<br /><br />Experimental Design: Following treatment failure patients with signed consent and aged above 6 months, underwent tumor biopsy or surgical resection of primary or metastatic tumor site.  These newly acquired samples were analyzed by comparative genomic hybridization array, next generation sequencing for 75 target genes, whole exome and RNA sequencing...
July 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28733429/proteogenomic-analysis-and-discovery-of-immune-antigens-in-mycobacterium-vaccae
#18
Jianhua Zheng, Lihong Chen, Liguo Liu, Haifeng Li, Bo Liu, Dandan Zheng, Tao Liu, Jie Dong, Lilian Sun, Yafang Zhu, Jian Yang, Xiaobing Zhang, Qi Jin
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M...
July 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28733194/breast-cancer-molecular-stratification-from-intrinsic-subtypes-to-integrative-clusters
#19
REVIEW
Hege G Russnes, Ole Christian Lingjærde, Anne-Lise Børresen-Dale, Carlos Caldas
Breast carcinomas can be stratified into different entities based on clinical behavior, histological features and/or by biological properties. A classification of breast cancer should be based on underlying biology, which we know must be determined by the somatic genomic landscape of mutations. Moreover, as the latest generations of anti-cancer agents are founded on biological mechanisms, a detailed molecular stratification is a requirement for appropriate clinical management. Such stratification, based on genomic drivers, will be important for selecting patients for clinical trials...
July 18, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28732532/gate-an-efficient-procedure-in-study-of-pleiotropic-genetic-associations
#20
Wei Zhang, Liu Yang, Larry L Tang, Aiyi Liu, James L Mills, Yuanchang Sun, Qizhai Li
BACKGROUND: The association studies on human complex traits are admittedly propitious to identify deleterious genetic markers. Compared to single-trait analyses, multiple-trait analyses can arguably make better use of the information on both traits and markers, and thus improve statistical power of association tests prominently. Principal component analysis (PCA) is a well-known useful tool in multivariate analysis and can be applied to this task. Generally, PCA is first performed on all traits and then a certain number of top principal components (PCs) that explain most of the trait variations are selected to construct the test statistics...
July 21, 2017: BMC Genomics
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