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genomic in practice

Héctor Cervera, Silvia Ambrós, Guillermo P Bernet, Guillermo Rodrigo, Santiago F Elena
Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus (TEV) that differ in fitness...
March 19, 2018: Molecular Biology and Evolution
Minseok Kwon, Sangseob Leem, Joon Yoon, Taesung Park
BACKGROUND: With the rapid advancement of array-based genotyping techniques, genome-wide association studies (GWAS) have successfully identified common genetic variants associated with common complex diseases. However, it has been shown that only a small proportion of the genetic etiology of complex diseases could be explained by the genetic factors identified from GWAS. This missing heritability could possibly be explained by gene-gene interaction (epistasis) and rare variants. There has been an exponential growth of gene-gene interaction analysis for common variants in terms of methodological developments and practical applications...
March 19, 2018: BMC Systems Biology
Washington Gapare, Shiming Liu, Warren Conaty, Qian-Hao Zhu, Vanessa Gillespie, Danny Llewellyn, Warwick Stiller, Iain Wilson
Genomic selection (GS) has successfully been used in plant breeding to improve selection efficiency and reduce breeding time and cost. However, there has not been a study to evaluate GS prediction models that may be used for predicting cotton breeding lines across multiple environments. In this study, we evaluated the performance of Bayes Ridge Regression, BayesA, BayesB, BayesC and Reproducing Kernel Hilbert Spaces regression models. We then extended the single-site GS model to accommodate genotype × environment interaction (G×E) in order to assess the merits of multi- over single-environment models in a practical breeding and selection context in cotton, a crop for which this has not previously been evaluated...
March 20, 2018: G3: Genes—Genomes—Genetics
Dwight D Bowman
Parasitology is a relevant and integral part of veterinary medicine, and the WAAVP membership has skills ranging from morphological diagnostics and routine parasite control recommendations through the cutting edges of many disciplines, e.g., pharmacology, immunology, molecular biology and genomics. We regularly face a majority of students who want only the practical information useful the moment they enter the clinics. However, we are preparing them for careers lasting 30-50 years. Thus, we also must help them prepare for their futures...
March 15, 2018: Veterinary Parasitology
Bin Guo, Baolin Wu
We propose statistical methods to detect novel genetic variants using only genome-wide association studies (GWAS) summary data without access to raw genotype and phenotype data. With more and more summary data being posted for public access in the post GWAS era, the proposed methods are practically very useful to identify additional interesting genetic variants and shed lights on the underlying disease mechanism. We illustrate the utility of our proposed methods with application to GWAS meta-analysis results of fasting glucose from the international MAGIC consortium...
March 1, 2018: Computational Biology and Chemistry
Han-Yu Jiang, Jin-Lin Zhang, Jiang-Wei Yang, Hui-Ling Ma
Creeping bentgrass ( Agrostis stolonifera ) is the preferred green lawn grass, with excellent turf characteristics but poor disease resistance. At present, the mechanisms of disease resistance in creeping bentgrass are poorly understood, especially the ethylene signal transduction pathway under the induced systemic resistance (ISR) response. In this study, butanediol (BDO), as a new type of disease-resistance compound, was applied to creeping bentgrass seedlings to induce the ISR response. Then, we measured ethylene production and related enzyme activities...
March 20, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Jerome Gnanaraj, Aric Parnes, Charles W Francis, Ronald S Go, Clifford M Takemoto, Shahrukh K Hashmi
Pancytopenia is a relatively common phenomenon encountered in clinical practice. The evaluation of a patient with pancytopenia requires a comprehensive approach and identifying the underlying cause can be challenging given the wide range of etiologies including drugs, autoimmune conditions, malignancies, infections, hemophagocytosis, and inheritable conditions. Recent advances in molecular hematology which include genomic profiling and next-generation sequencing have helped gain major insights into various hematological conditions and can guide diagnosing specific diseases in a shorter time at lower costs...
March 5, 2018: Blood Reviews
J M Cozar, I Robles-Fernandez, L J Martinez-Gonzalez, M Pascual-Geler, Alba Rodriguez-Martinez, M J Serrano, J A Lorente, M J Alvarez-Cubero
Prostate cancer (PC) is one of the most common cancers worldwide. The observed variability in progression and responses to the same treatment between patients underlie the genetic heterogeneity of the disease. Nowadays, screening and follow-up biomarkers in PC are still having a deep lack of information, which makes difficult the cancer diagnosis, prognosis and the selection of the most suitable therapies. This is making that currently unnecessary biopsies, over-treatments and hormonoresistances have high rates of prevalence among patients...
January 2018: Mutation Research
D A Kenny, C J Byrne
The advent of genomic selection has led to increased interest within the cattle breeding industry to market semen from young bulls as early as possible. However, both the quantity and quality of such semen is dictated by the age at which these animals reach puberty. Enhancing early life plane of nutrition of the bull stimulates a complex biochemical interplay involving metabolic and neuroendocrine signalling and culminating in enhanced testicular growth and development and earlier onset of sexual maturation...
March 20, 2018: Animal: An International Journal of Animal Bioscience
Hyoungnae Kim, Misol Lee, Min-Uk Cha, Ki Heon Nam, Seong Yeong An, Seohyun Park, Jong Hyun Jhee, Hae-Ryong Yun, Youn Kyung Kee, Jung Tak Park, Tae-Hyun Yoo, Shin-Wook Kang, Seung Hyeok Han
Background: Although asymptomatic microscopic hematuria (MH) is a common finding in clinical practice, its long-term outcome remains unknown. Aim: This study evaluated the clinical implication of MH in the general population using a large-scale long-term longitudinal cohort database. Methods: This study included 8719 participants from the Korean Genome and Epidemiology Study between 2001 and 2014. MH was defined as ≥ 5 red blood cells per high-power field in random urinalysis without evidence of pyuria...
March 14, 2018: QJM: Monthly Journal of the Association of Physicians
Rainer Malik, Martin Dichgans
Stroke, ischemic stroke and subtypes of ischemic stroke display substantial heritability. Compared to related vascular conditions, the number of established risk loci reaching genome-wide significance for association with stroke is still in the lower range, particularly for etiological stroke subtypes such as large artery atherosclerotic stroke or small vessel stroke. Nevertheless, for individual loci substantial progress has been made in determining the specific mechanisms mediating stroke risk. In this review, we present a roadmap for functional follow-up of common risk variants associated with stroke...
March 15, 2018: Cardiovascular Research
Vasiliki Rahimzadeh, Christoph Schickhardt, Bartha M Knoppers, Karine Sénécal, Danya F Vears, Conrad V Fernandez, Stefan Pfister, Sharon Plon, Sharon Terry, Janet Williams, Marc S Williams, Martina Cornel, Jan M Friedman
Accurate clinical interpretation of children's whole-genome and whole-exome sequences relies on comparing the patient's linked genomic and phenotypic data with variant reference databases of both healthy and affected patients. The robustness of such comparisons, in turn, is made possible by sharing pediatric genomic and associated clinical data. Despite this, sparse ethical-legal policy attention has been paid to making such sharing routine in practice. The interdisciplinary Paediatric Task Team of the Global Alliance for Genomics and Health considered in detail the current ethical, legal, and social implications of sharing genomic and associated clinical data involving children...
March 19, 2018: JAMA Pediatrics
Chang Xu
Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology. A collection of variant calling pipelines have been developed with different underlying models, filters, input data requirements, and targeted applications. This review aims to enumerate these unique features of the state-of-the-art variant callers, in the hope to provide a practical guide for selecting the appropriate pipeline for specific applications...
2018: Computational and Structural Biotechnology Journal
John F Brothers, Matthew Ung, Renan Escalante-Chong, Jermaine Ross, Jenny Zhang, Yoonjeong Cha, Andrew Lysaght, Jason Funt, Rebecca Kusko
The tremendous expansion of data analytics and public and private big datasets presents an important opportunity for pre-clinical drug discovery and development. In the field of life sciences, the growth of genetic, genomic, transcriptomic and proteomic data is partly driven by a rapid decline in experimental costs as biotechnology improves throughput, scalability, and speed. Yet far too many researchers tend to underestimate the challenges and consequences involving data integrity and quality standards. Given the effect of data integrity on scientific interpretation, these issues have significant implications during preclinical drug development...
March 15, 2018: Biochemical Pharmacology
Zhong-Feng Li, Yong Guo, Lin Ou, Huilong Hong, Jun Wang, Zhang-Xiong Liu, Bingfu Guo, Lijuan Zhang, Lijuan Qiu
GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length...
March 17, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Wouter Saelens, Robrecht Cannoodt, Yvan Saeys
A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modelling the regulatory network, and/or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods...
March 15, 2018: Nature Communications
Kathleen A Calzone, Jean Jenkins, Stacey Culp, Laurie Badzek
BACKGROUND: The Precision Medicine Initiative will accelerate genomic discoveries that improve health care, necessitating a genomic competent workforce. PURPOSE: This study assessed leadership team (administrator/educator) year-long interventions to improve registered nurses' (RNs) capacity to integrate genomics into practice. METHODS: We examined genomic competency outcomes in 8,150 RNs. DISCUSSION: Awareness and intention to learn more increased compared with controls...
November 13, 2017: Nursing Outlook
Renata C Gallagher, Laura Pollard, Anna I Scott, Suzette Huguenin, Stephen Goodman, Qin Sun
Disclaimer: These ACMG Standards are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards is voluntary and does not necessarily assure a successful medical outcome. These Standards should not be considered inclusive of all proper procedures and tests, or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen...
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Lucía Fernández, Alejandra Leivas, Jaime Valentín, Adela Escudero, Dolores Corral, Raquel de Paz, Maria Vela, David Bueno, Rebeca Rodríguez, Juan Manuel Torres, Mariana Díaz-Almirón, Eduardo López-Collazo, Joaquin Martinez-Lopez, Antonio Pérez-Martínez
BACKGROUND: Cancer immunotherapy involving natural killer (NK) cells has gained interest. Here we report two methods to obtain interleukin (IL)-15-activated NK cells for clinical use. STUDY DESIGN AND METHODS: IL-15-activated NK cell products were obtained after 1) enrichment from healthy haploidentical donors' peripheral blood mononuclear cells (PBMNCs) collected by nonmobilized apheresis by a two-step magnetic procedure, depletion of CD3+ cells followed by selection of CD56+ cells and ex vivo overnight stimulation with IL-15 (NKIL15); and 2) expansion using the K562-mb15-41BBL cell line (NKAE), from autologous PBMNCs from patients with multiple myeloma or expansion from healthy haploidentical PBMNCs obtained from whole blood using the same previous cell line...
March 14, 2018: Transfusion
Hitoyoshi Yasuo, Alex McDougall
Phallusia mammillata has recently emerged as a new ascidian model. Its unique characteristics, including the optical transparency of eggs and embryos and efficient translation of exogenously introduced mRNA in eggs, make the Phallusia system suitable for fluorescent protein (FP)-based imaging approaches. In addition, genomic and transcriptomic resources are readily available for this ascidian species, facilitating functional gene studies. Microinjection is probably the most versatile technique for introducing exogenous molecules such as plasmids, mRNAs, and proteins into ascidian eggs/embryos...
2018: Advances in Experimental Medicine and Biology
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