keyword
MENU ▼
Read by QxMD icon Read
search

genomic in practice

keyword
https://www.readbyqxmd.com/read/28340465/dumbbell-dna-templated-cunps-as-a-nano-fluorescent-probe-for-detection-of-enzymes-involved-in-ligase-mediated-dna-repair
#1
Taiping Qing, Xiaoxiao He, Dinggeng He, Xiaosheng Ye, Jingfang Shangguan, Jinquan Liu, Baoyin Yuan, Kemin Wang
DNA repair processes are responsible for maintaining genome stability. Ligase and polynucleotide kinase (PNK) have important roles in ligase-mediated DNA repair. The development of analytical methods to monitor these enzymes involved in DNA repair pathways is of great interest in biochemistry and biotechnology. In this work, we reported a new strategy for label-free monitoring PNK and ligase activity by using dumbbell-shaped DNA templated copper nanoparticles (CuNPs). In the presence of PNK and ligase, the dumbbell-shaped DNA probe (DP) was locked and could resist the digestion of exonucleases and then served as an efficient template for synthesizing fluorescent CuNPs...
March 21, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28339749/multi-generational-genome-wide-association-studies-identify-chromosomal-regions-associated-with-ascites-phenotype
#2
K J Tarrant, S Dey, R Kinney, N B Anthony, D D Rhoads
Ascites is a multi-faceted disease commonly observed in fast growing broilers, which is initiated when the body is insufficiently oxygenated. A series of events follow, including an increase in pulmonary artery pressure, right ventricle hypertrophy, and accumulation of fluid in the abdominal cavity and pericardium. Advances in management practices along with improved selection programs have decreased ascites incidence in modern broilers. However, ascites syndrome remains an economically important disease throughout the world, causing estimated losses of $100 million per year...
February 21, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339689/genomic-decision-support-needs-in-pediatric-primary-care
#3
Jeffrey W Pennington, Dean J Karavite, Edward M Krause, Jeffrey Miller, Barbara A Bernhardt, Robert W Grundmeier
Clinical genome and exome sequencing can diagnose pediatric patients with complex conditions that often require follow-up care with multiple specialties. The American Academy of Pediatrics emphasizes the role of the medical home and the primary care pediatrician in coordinating care for patients who need multidisciplinary support. In addition, the electronic health record (EHR) with embedded clinical decision support is recognized as an important component in providing care in this setting. We interviewed 6 clinicians to assess their experience caring for patients with complex and rare genetic findings and hear their opinions about how the EHR currently supports this role...
February 19, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28339683/addressing-beacon-re-identification-attacks-quantification-and-mitigation-of-privacy-risks
#4
Jean Louis Raisaro, Florian Tramèr, Zhanglong Ji, Diyue Bu, Yongan Zhao, Knox Carey, David Lloyd, Heidi Sofia, Dixie Baker, Paul Flicek, Suyash Shringarpure, Carlos Bustamante, Shuang Wang, Xiaoqian Jiang, Lucila Ohno-Machado, Haixu Tang, XiaoFeng Wang, Jean-Pierre Hubaux
The Global Alliance for Genomics and Health (GA4GH) created the Beacon Project as a means of testing the willingness of data holders to share genetic data in the simplest technical context-a query for the presence of a specified nucleotide at a given position within a chromosome. Each participating site (or "beacon") is responsible for assuring that genomic data are exposed through the Beacon service only with the permission of the individual to whom the data pertains and in accordance with the GA4GH policy and standards...
February 20, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28338774/pleiotropy-robust-mendelian-randomization
#5
Hans van Kippersluis, Cornelius A Rietveld
Background: The potential of Mendelian randomization studies is rapidly expanding due to: (i) the growing power of genome-wide association study (GWAS) meta-analyses to detect genetic variants associated with several exposures; and (ii) the increasing availability of these genetic variants in large-scale surveys. However, without a proper biological understanding of the pleiotropic working of genetic variants, a fundamental assumption of Mendelian randomization (the exclusion restriction) can always be contested...
February 22, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/28337931/utilizing-nutritional-genomics-to-tailor-diets-for-the-prevention-of-cardiovascular-disease-a-guide-for-upcoming-studies-and-implementations
#6
Dolores Corella, Oscar Coltell, George Mattingley, José V Sorlí, Jose M Ordovas
Personalized diets based on an individual's genome to optimize the success of dietary intervention and reduce genetic cardiovascular disease (CVD) risk, is one of the challenges most frequently discussed in the scientific community. Areas covered: The authors gathered literature-based evidence on nutritional genomics and CVD phenotypes, our own results and research experience to provide a critical overview of the current situation of using nutritional genomics to tailor diets for CVD prevention and to propose guidelines for future studies and implementations...
March 24, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28335731/highly-diverse-population-of-picornaviridae-and-other-members-of-the-picornavirales-in-cameroonian-fruit-bats
#7
Claude Kwe Yinda, Roland Zell, Ward Deboutte, Mark Zeller, Nádia Conceição-Neto, Elisabeth Heylen, Piet Maes, Nick J Knowles, Stephen Mbigha Ghogomu, Marc Van Ranst, Jelle Matthijnssens
BACKGROUND: The order Picornavirales represents a diverse group of positive-stranded RNA viruses with small non-enveloped icosahedral virions. Recently, bats have been identified as an important reservoir of several highly pathogenic human viruses. Since many members of the Picornaviridae family cause a wide range of diseases in humans and animals, this study aimed to characterize members of the order Picornavirales in fruit bat populations located in the Southwest region of Cameroon...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28334972/enrichment-methods-provide-a-feasible-approach-to-comprehensive-and-adequately-powered-investigations-of-the-brain-methylome
#8
Robin F Chan, Andrey A Shabalin, Lin Y Xie, Daniel E Adkins, Min Zhao, Gustavo Turecki, Shaunna L Clark, Karolina A Aberg, Edwin J C G van den Oord
Methylome-wide association studies are typically performed using microarray technologies that only assay a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is to use whole genome bisulfite (WGB) sequencing but this approach is not yet practically feasible with sample sizes required for adequate statistical power. We argue for revisiting methylation enrichment methods that, provided optimal protocols are used, enable comprehensive, adequately powered and cost-effective genome-wide investigations of the brain methylome...
February 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334086/pseudoalignment-for-metagenomic-read-assignment
#9
L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter
Motivation: Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains...
February 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334077/a-powerful-and-efficient-two-stage-method-for-detecting-gene-to-gene-interactions-in-gwas
#10
Jakub Pecanka, Marianne A Jonker, Zoltan Bochdanovits, Aad W Van Der Vaart
For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the "missing heritability" of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype...
February 6, 2017: Biostatistics
https://www.readbyqxmd.com/read/28333396/conflicting-phylogenomic-signals-reveal-a-pattern-of-reticulate-evolution-in-a-recent-high-andean-diversification-asteraceae-astereae-diplostephium
#11
Oscar M Vargas, Edgardo M Ortiz, Beryl B Simpson
High-throughput sequencing is helping biologists to overcome the difficulties of inferring the phylogenies of recently diverged taxa. The present study analyzes the phylogenetic signal of genomic regions with different inheritance patterns using genome skimming and ddRAD-seq in a species-rich Andean genus (Diplostephium) and its allies. We analyzed the complete nuclear ribosomal cistron, the complete chloroplast genome, a partial mitochondrial genome, and a nuclear-ddRAD matrix separately with phylogenetic methods...
March 23, 2017: New Phytologist
https://www.readbyqxmd.com/read/28333293/intra-individual-purifying-selection-on-mitochondrial-dna-variants-during-human-oogenesis
#12
Sara De Fanti, Saverio Vicario, Martin Lang, Domenico Simone, Cristina Magli, Donata Luiselli, Luca Gianaroli, Giovanni Romeo
Study Question: Does selection for mtDNA mutations occur in human oocytes? Summary Answer: We provide statistical evidence in favor of the existence of purifying selection for mtDNA mutations in human oocytes acting between the expulsion of the first and second polar bodies (PBs). What is Known Already: Several lines of evidence in Metazoa, including humans, indicate that variation within the germline of mitochondrial genomes is under purifying selection...
March 9, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28333245/euploidy-rates-in-donor-egg-cycles-significantly-differ-between-fertility-centers
#13
S Munné, M Alikani, L Ribustello, P Colls, Pedro A Martínez-Ortiz, D H McCulloh
STUDY QUESTION: Do external factors affect euploidy in egg donor cycles? SUMMARY ANSWER: The study demonstrates that during human assisted reproduction, embryonic chromosome abnormalities may be partly iatrogenic. WHAT IS KNOWN ALREADY: Chromosome abnormalities have been linked in the past to culture conditions such as temperature and Ph variations, as well as hormonal stimulation. Those reports were performed with older screening techniques (FISH), or ART methods no longer in use, and the subjects studied were not a homogeneous group...
March 2, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28330894/targeted-enrichment-for-pathogen-detection-and-characterization-in-three-felid-species
#14
Justin S Lee, Ryan S Mackie, Thomas Harrison, Basir Shariat, Trey Kind, Timo Kehl, Martin Löchelt, Christina Boucher, Sue VandeWoude
Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application detecting low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While prior studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting has not yet been evaluated...
March 22, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28330454/uncovering-snp-and-indel-variations-of-tetraploid-cottons-by-slaf-seq
#15
Chao Shen, Xin Jin, De Zhu, Zhongxu Lin
BACKGROUND: Cotton (Gossypium spp.), as the world's most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for exploitation of the excellent characteristics of wild cotton and for improving the diversity of cotton in breeding. However, the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged behind other important crops. RESULTS: A total of 111,795,823 reads, 467,735 specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA polymorphisms were identified using specific length amplified fragment sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the reference genome (TM-1) and the five tetraploid cotton species...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28330383/progress-in-nonviral-gene-therapy-for-breast-cancer-and-what-comes-next
#16
Giulia Bottai, Marta Truffi, Fabio Corsi, Libero Santarpia
The possibility of correcting defective genes and modulating gene expression through gene therapy has emerged as a promising treatment strategy for breast cancer. Furthermore, the relevance of tumor immune microenvironment in supporting the oncogenic process has paved the way for novel immunomodulatory applications of gene therapy. Areas covered: In this review, the authors describe the most relevant delivery systems, focusing on nonviral vectors, along with the description of the major approaches used to modify target cells, including gene transfer, RNA interference (RNAi), and epigenetic regulation...
March 22, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/28328372/psychiatric-genomics-and-mental-health-treatment-setting-the-ethical-agenda
#17
Camillia Kong, Michael Dunn, Michael Parker
Realizing the benefits of translating psychiatric genomics research into mental health care is not straightforward. The translation process gives rise to ethical challenges that are distinctive from challenges posed within psychiatric genomics research itself, or that form part of the delivery of clinical psychiatric genetics services. This article outlines and considers three distinct ethical concerns posed by the process of translating genomic research into frontline psychiatric practice and policy making...
April 2017: American Journal of Bioethics: AJOB
https://www.readbyqxmd.com/read/28327976/minion%C3%A2-nanopore-sequencing-of-environmental-metagenomes-a-synthetic-approach
#18
Bonnie L Brown, Mick Watson, Samuel S Minot, Maria C Rivera, Rima B Franklin
Background: Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing (WGS) or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1×10 4 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327897/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#19
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
February 3, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28327572/the-role-of-genetic-counsellors-in-genomic-healthcare-in-the-united-kingdom-a-statement-by-the-association-of-genetic-nurses-and-counsellors
#20
Anna Middleton, Peter Marks, Anita Bruce, Liwsi K Protheroe-Davies, Cath King, Oonagh Claber, Catherine Houghton, Claire Giffney, Rhona Macleod, Claire Dolling, Sue Kenwrick, Diana Scotcher, Georgina Hall, Christine Patch, Laura Boyes
In the United Kingdom, genetic counsellors work together with clinical geneticists and clinical scientist colleagues within specialist genetics services, but they also often work in multidisciplinary teams (MDTs) outside of such services. There, they contribute genetic knowledge together with expert understanding of how to communicate genetic information effectively. They can offer education and support to the MDT, while providing management advice for both affected patients and the extended at-risk family members...
March 22, 2017: European Journal of Human Genetics: EJHG
keyword
keyword
107441
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"