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https://www.readbyqxmd.com/read/28921878/simplifying-sampling-for-african-swine-fever-surveillance-assessment-of-antibody-and-pathogen-detection-from-blood-swabs
#1
J Carlson, L Zani, T Schwaiger, I Nurmoja, A Viltrop, A Vilem, M Beer, S Blome
African swine fever (ASF) is a notifiable disease with serious socio-economic consequences that has been present in wild boar in the Baltic States and Poland since 2014. An introduction of ASF is usually accompanied by increased mortality, making fallen wild boar and hunted animals with signs of disease the main target for early warning and passive surveillance. It is difficult, however, to encourage hunters and foresters to report and take samples from these cases. A pragmatic and easy sampling approach with quick-drying swabs could facilitate this...
September 17, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28921651/somatic-mutation-analysis-of-human-cancers-challenges-in-clinical-practice
#2
Gregory J Tsongalis, William B Coleman
Somatic mutation analysis of human cancers has become the standard of practice. Whether screening for single gene variants or sequencing hundreds of cancer-related genes, this genomic information is the basis for precision medicine initiatives in oncology. Genomic profiling results in information that allows oncologists to make a more educated selection of appropriate therapeutic strategies that more often combine traditional cytotoxic chemotherapy and radiation with novel targeted therapies. Here we discuss the nuances of implementing somatic mutation testing in a clinical setting...
October 2017: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28920489/primer-in-genetics-and-genomics-article-5-further-defining-the-concepts-of-genotype-and-phenotype-and-exploring-genotype-phenotype-associations
#3
Fay Wright, Kristen Fessele
As nurses begin to incorporate genetic and genomic sciences into clinical practice, education, and research, it is essential that they have a working knowledge of the terms foundational to the science. The first article in this primer series provided brief definitions of the basic terms (e.g., genetics and genomics) and introduced the concept of phenotype during the discussion of Mendelian inheritance. These terms, however, are inconsistently used in publications and conversations, and the linkage between genotype and phenotype requires clarification...
October 2017: Biological Research for Nursing
https://www.readbyqxmd.com/read/28919992/molecular-and-clinical-characterization-of-tim-3-in-glioma-through-1-024-samples
#4
Guanzhang Li, Zheng Wang, Chuanbao Zhang, Xing Liu, Jinquan Cai, Zhiliang Wang, Huimin Hu, Fan Wu, Zhaoshi Bao, Yanwei Liu, Liang Zhao, Tingyu Liang, Fan Yang, Ruoyu Huang, Wei Zhang, Tao Jiang
Background: Researches on immunotherapy of glioma has been increasing exponentially in recent years. However, autoimmune-like side effects of current immune checkpoint blockade hindered the clinical application of immunotherapy in glioma. The discovery of the TIM-3, a tumor-specific immune checkpoint, has shed a new light on solution of this dilemma. We aimed at investigating the role of TIM-3 at transcriptome level and its relationship with clinical practice in glioma. Methods: A cohort of 325 glioma patients with RNA-seq data from Chinese Glioma Genome Atlas (CGGA project) was analyzed, and the results were well validated in TCGA RNA-seq data of 699 gliomas...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28918100/transcriptomic-and-epigenomic-biomarkers-of-antidepressant-response
#5
REVIEW
Raoul Belzeaux, Rixing Lin, Chelsey Ju, Marc-Aurele Chay, Laura M Fiori, Pierre-Eric Lutz, Gustavo Turecki
BACKGROUND: Antidepressant treatment is associated with a high rate of poor response, and thus, biomarker development is warranted. METHODS: We aimed to synthesize studies investigating gene expression, small RNAs, and epigenomic biomarkers of antidepressant response. We conducted a narrative review of the literature. RESULTS: Firstly, we detailed the challenges involved, in terms of biological tissues, relevant study time frames, and mandatory statistical tools...
September 8, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28916928/newborn-screening-in-the-era-of-precision-medicine
#6
Lan Yang, Jiajia Chen, Bairong Shen
As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916649/genomic-prediction-within-and-across-biparental-families-means-and-variances-of-prediction-accuracy-and-usefulness-of-deterministic-equations
#7
Pascal Schopp, Dominik Müller, Yvonne C J Wientjes, Albrecht E Melchinger
A major application of genomic prediction (GP) in plant breeding is the identification of superior inbred lines within families derived from biparental crosses. When models for various traits were trained within related or unrelated biparental families (BPFs), experimental studies found substantial variation in prediction accuracy (PA), but little is known about the underlying factors. We used SNP marker genotypes of inbred lines from either elite germplasm or landraces of maize (Zea mays L.) as parents to generate in silico 300 BPFs of doubled-haploid lines...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28915902/development-and-clinical-application-of-radiomics-in-lung-cancer
#8
REVIEW
Bojiang Chen, Rui Zhang, Yuncui Gan, Lan Yang, Weimin Li
Since the discovery of X-rays at the end of the 19(th) century, medical imageology has progressed for 100 years, and medical imaging has become an important auxiliary tool for clinical diagnosis. With the launch of the human genome project (HGP) and the development of various high-throughput detection techniques, disease exploration in the post-genome era has extended beyond investigations of structural changes to in-depth analyses of molecular abnormalities in tissues, organs and cells, on the basis of gene expression and epigenetics...
September 15, 2017: Radiation Oncology
https://www.readbyqxmd.com/read/28914268/impact-of-hipaa-s-minimum-necessary-standard-on-genomic-data-sharing
#9
Barbara J Evans, Gail P Jarvik
This article provides a brief introduction to the Health Insurance Portability and Accountability Act of 1996 (HIPAA) Privacy Rule's minimum necessary standard, which applies to sharing of genomic data, particularly clinical data, following 2013 Privacy Rule revisions. This research used the Thomson Reuters Westlaw database and law library resources in its legal analysis of the HIPAA privacy tiers and the impact of the minimum necessary standard on genomic data sharing. We considered relevant example cases of genomic data-sharing needs...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28914267/developing-a-common-framework-for-evaluating-the-implementation-of-genomic-medicine-interventions-in-clinical-care-the-ignite-network-s-common-measures-working-group
#10
Lori A Orlando, Nina R Sperber, Corrine Voils, Marshall Nichols, Rachel A Myers, R Ryanne Wu, Tejinder Rakhra-Burris, Kenneth D Levy, Mia Levy, Toni I Pollin, Yue Guan, Carol R Horowitz, Michelle Ramos, Stephen E Kimmel, Caitrin W McDonough, Ebony B Madden, Laura J Damschroder
PurposeImplementation research provides a structure for evaluating the clinical integration of genomic medicine interventions. This paper describes the Implementing Genomics in Practice (IGNITE) Network's efforts to promote (i) a broader understanding of genomic medicine implementation research and (ii) the sharing of knowledge generated in the network.MethodsTo facilitate this goal, the IGNITE Network Common Measures Working Group (CMG) members adopted the Consolidated Framework for Implementation Research (CFIR) to guide its approach to identifying constructs and measures relevant to evaluating genomic medicine as a whole, standardizing data collection across projects, and combining data in a centralized resource for cross-network analyses...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28913944/the-more-you-test-the-more-you-find-the-smallest-p-values-become-increasingly-enriched-with-real-findings-as-more-tests-are-conducted
#11
Olga A Vsevolozhskaya, Chia-Ling Kuo, Gabriel Ruiz, Luda Diatchenko, Dmitri V Zaykin
The increasing accessibility of data to researchers makes it possible to conduct massive amounts of statistical testing. Rather than follow specific scientific hypotheses with statistical analysis, researchers can now test many possible relationships and let statistics generate hypotheses for them. The field of genetic epidemiology is an illustrative case, where testing of candidate genetic variants for association with an outcome has been replaced by agnostic screening of the entire genome. Poor replication rates of candidate gene studies have improved dramatically with the increase in genomic coverage, due to factors such as adoption of better statistical practices and availability of larger sample sizes...
September 14, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28912897/genomic-analysis-of-tumor-microenvironment-immune-types-across-14-solid-cancer-types-immunotherapeutic-implications
#12
Yu-Pei Chen, Yu Zhang, Jia-Wei Lv, Ying-Qin Li, Ya-Qin Wang, Qing-Mei He, Xiao-Jing Yang, Ying Sun, Yan-Ping Mao, Jing-Ping Yun, Na Liu, Jun Ma
We performed a comprehensive immuno-genomic analysis of tumor microenvironment immune types (TMITs), which is classified into four groups based on PD-L1+CD8A or PD-L1+cytolytic activity (CYT) expression, across a broad spectrum of solid tumors in order to help identify patients who will benefit from anti- PD-1/PD-L1 therapy. The mRNA sequencing data from The Cancer Genome Atlas (TCGA) of 14 solid cancer types representing 6,685 tumor samples was analyzed. TMIT was classified only for those tumor types that both PD-L1 and CD8A/CYT could prefict mutation and/or neoantigen number...
2017: Theranostics
https://www.readbyqxmd.com/read/28912793/diverse-rice-landraces-of-north-east-india-enables-the-identification-of-novel-genetic-resources-for-magnaporthe-resistance
#13
Bangale Umakanth, Balija Vishalakshi, P Sathish Kumar, S J S Rama Devi, Vijay Pal Bhadana, P Senguttuvel, Sudhir Kumar, Susheel Kumar Sharma, Pawan Kumar Sharma, M S Prasad, Maganti S Madhav
North-East (NE) India, the probable origin of rice has diverse genetic resources. Many rice landraces of NE India were not yet characterized for blast resistance. A set of 232 landraces of NE India, were screened for field resistance at two different hotspots of rice blast, viz., IIRR-UBN, Hyderabad and ICAR-NEH, Manipur in two consecutive seasons. The phenotypic evaluation as well as gene profiling for 12 major blast resistance genes (Pitp, Pi33, Pi54, Pib, Pi20, Pi38, Pita2, Pi1, Piz, Pi9, Pizt, and Pi40) with linked as well as gene-specific markers, identified 84 resistant landraces possessing different gene(s) either in singly or in combinations and also identified seven resistant landraces which do not have the tested genes, indicating the valuable genetic resources for blast resistance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28904262/biodegradation-of-volatile-organic-compounds-and-their-effects-on-biodegradability-under-co-existing-conditions
#14
Miho Yoshikawa, Ming Zhang, Koki Toyota
Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs...
September 12, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28903902/single-cell-gene-variation-analysis-method-for-single-gland
#15
Yan Zhou, Chao-Jie Wang, Chun-Chao Zhu, Jiang-Rong Chen, Ming Cheng, Yu-Liang Deng, Yan Guo
Single-cell analysis of heterogeneity has become the cutting-edge technology for profound understandings of relationships between cell populations. At present, common methods used in single cellular genomic research are mainly microfluidic technologies (Fluidigm) or based on microwells, both requiring a uniform size of cells at the entrance. However, the size of cells in specific tissues can vary from type to type. To address this issue, we need to establish a method to identify genomic features of individual cells of different sizes...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28900437/genetics-of-resistance-and-pathogenicity-in-the-maize-setosphaeria-turcica-pathosystem-and-implications-for-breeding
#16
REVIEW
Ana L Galiano-Carneiro, Thomas Miedaner
Northern corn leaf blight (NCLB), the most devastating leaf pathogen in maize (Zea mays L.), is caused by the heterothallic ascomycete Setosphaeria turcica. The pathogen population shows an extremely high genetic diversity in tropical and subtropical regions. Varietal resistance is the most efficient technique to control NCLB. Host resistance can be qualitative based on race-specific Ht genes or quantitative controlled by many genes with small effects. Quantitative resistance is moderately to highly effective and should be more durable combatting all races of the pathogen...
2017: Frontiers in Plant Science
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
#17
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/28899997/improving-disease-prediction-by-incorporating-family-disease-history-in-risk-prediction-models-with-large-scale-genetic-data
#18
Jungsoo Gim, Wonji Kim, Soo Heon Kwak, Hosik Choi, Changyi Park, Kyong Soo Park, Sunghoon Kwon, Taesung Park, Sungho Won
Despite the many successes of genome-wide association studies (GWAS), the known susceptibility variants identified by GWAS have modest effect sizes, leading to notable skepticism about the effectiveness of building a risk prediction model from large-scale genetic data. However, in contrast to genetic variants, the family history of diseases has been largely accepted as an important risk factor in clinical diagnosis and risk prediction. Nevertheless, the complicated structures of the family history of diseases have limited their application in clinical practice...
September 12, 2017: Genetics
https://www.readbyqxmd.com/read/28890089/-tumour-sequencing-evolutions-and-revolutions
#19
N Piton, A Lamy, J-C Sabourin
For some years now, we have entered the genomic age of tumour genotyping from a medical point of view. Technological breakthroughs in both biology and information science now allow a genomic analysis of cancers in everyday medical practice with, in some case, a major impact on patient care not only for the choice of therapy (i.e. EGFR mutations in lung adenocarcinoma), but also for diagnosis and monitoring of the disease. Tumour genotyping is performed from formalin-fixed paraffin-embedded tissues used for diagnosis of cancer...
September 7, 2017: Cancer Radiothérapie: Journal de la Société Française de Radiothérapie Oncologique
https://www.readbyqxmd.com/read/28888961/the-seqan-c-template-library-for-efficient-sequence-analysis-a-resource-for-programmers
#20
Knut Reinert, Temesgen Hailemariam Dadi, Marcel Ehrhardt, Hannes Hauswedell, Svenja Mehringer, René Rahn, Jongkyu Kim, Christopher Pockrandt, Jörg Winkler, Enrico Siragusa, Gianvito Urgese, David Weese
BACKGROUND: The use of novel algorithmic techniques is pivotal to many important problems in life science. For example the sequencing of the human genome (Venter et al., 2001) would not have been possible without advanced assembly algorithms and the development of practical BWT based read mappers have been instrumental for NGS analysis. However, owing to the high speed of technological progress and the urgent need for bioinformatics tools, there was a widening gap between state-of-the-art algorithmic techniques and the actual algorithmic components of tools that are in widespread use...
September 6, 2017: Journal of Biotechnology
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