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https://www.readbyqxmd.com/read/28544474/breast-cancer-and-transplantation
#1
Germaine Wong, Eric Au, Sunil V Badve, Wai H Lim
Breast cancer is an important cancer among solid organ transplant recipients. While the incidence of breast cancer in solid organ transplant recipients is comparable to the age matched general population, the outcomes are generally poor. Interventions such as cancer screening which preclude the development of late stage disease through early detection are not well-studied, and clinical practice guidelines for cancer screening rely solely on recommendations from the general population. Among those with a prior breast cancer history, disease recurrence after transplantation is a rare but fearful event...
May 19, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#2
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28533195/de-novo-8p23-1-deletion-in-a-patient-with-absence-epilepsy
#3
Nihan Hande Akcakaya, Özlem Yalcin Capan, Herbert Schulz, Thomas Sander, Server Hande Caglayan, Zuhal Yapıcı
The 8p23.1 deletion syndrome is a rare multisystem disorder with high penetrance and a variable phenotypic spectrum that includes congenital heart disease (CHD), intellectual disability, behavioural problems, microcephalia, and sometimes epilepsy. Genomic copy number variations (CNVs) constitute an important genetic risk factor for common genetic generalised epilepsy syndromes (GGEs) and absence seizures. These variations, resulting either from copy loss (microdeletion) or copy gain (duplications), disrupt genes associated with neuronal development...
May 22, 2017: Epileptic Disorders: International Epilepsy Journal with Videotape
https://www.readbyqxmd.com/read/28532511/challenges-and-strategies-for-implementing-genomic-services-in-diverse-settings-experiences-from-the-implementing-genomics-in-practice-ignite-network
#4
Nina R Sperber, Janet S Carpenter, Larisa H Cavallari, Laura J Damschroder, Rhonda M Cooper-DeHoff, Joshua C Denny, Geoffrey S Ginsburg, Yue Guan, Carol R Horowitz, Kenneth D Levy, Mia A Levy, Ebony B Madden, Michael E Matheny, Toni I Pollin, Victoria M Pratt, Marc Rosenman, Corrine I Voils, Kristen W Weitzel, Russell A Wilke, R Ryanne Wu, Lori A Orlando
BACKGROUND: To realize potential public health benefits from genetic and genomic innovations, understanding how best to implement the innovations into clinical care is important. The objective of this study was to synthesize data on challenges identified by six diverse projects that are part of a National Human Genome Research Institute (NHGRI)-funded network focused on implementing genomics into practice and strategies to overcome these challenges. METHODS: We used a multiple-case study approach with each project considered as a case and qualitative methods to elicit and describe themes related to implementation challenges and strategies...
May 22, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28532404/use-of-the-qiagen-genereader-ngs-system-for-detection-of-kras-mutations-validated-by-the-qiagen-therascreen-pcr-kit-and-alternative-ngs-platform
#5
Agus Darwanto, Anne-Mette Hein, Sascha Strauss, Yi Kong, Andrew Sheridan, Dan Richards, Eric Lader, Monika Ngowe, Timothy Pelletier, Danielle Adams, Austin Ricker, Nishit Patel, Andreas Kühne, Simon Hughes, Dan Shiffman, Dirk Zimmermann, Kai Te Kaat, Thomas Rothmann
BACKGROUND: The detection of somatic mutations in primary tumors is critical for the understanding of cancer evolution and targeting therapy. Multiple technologies have been developed to enable the detection of such mutations. Next generation sequencing (NGS) is a new platform that is gradually becoming the technology of choice for genotyping cancer samples, owing to its ability to simultaneously interrogate many genomic loci at massively high efficiency and increasingly lower cost. However, multiple barriers still exist for its broader adoption in clinical research practice, such as fragmented workflow and complex bioinformatics analysis and interpretation...
May 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28527664/a-new-hdv-mouse-model-identifies-mitochondrial-antiviral-signaling-protein-mavs-as-a-key-player-in-ifn-%C3%AE-induction
#6
Lester Suárez-Amarán, Carla Usai, Marianna Di Scala, Cristina Godoy, Yi Ni, Mirja Hommel, Laura Palomo, Víctor Segura, Cristina Olagüe, Africa Vales, Alicia Ruiz-Ripa, Maria Buti, Eduardo Salido, Jesús Prieto, Stephan Urban, Francisco Rodríguez-Frias, Rafael Aldabe, Gloria González-Aseguinolaza
BACKGROUND & AIMS: Studying hepatitis delta virus (HDV) and developing new treatments is hampered by the limited availability of small animal models. Here a description of a robust mouse model of HDV infection that mimics several important characteristics of the human disease is presented. METHODS: HDV- and HBV-replication competent genomes were delivered to the mouse liver using adeno-associated viruses (AAV) (AAV-HDV and AAV-HBV). Viral load, antigen expression and genomes were quantified at different time points after AAV injection...
May 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28527373/-i-don-t-believe-it-acceptance-and-skepticism-of-genetic-health-information-among-african-american-and-white-smokers
#7
Erika A Waters, Linda Ball, Sarah Gehlert
RATIONALE: Effective translation of genomics research into practice depends on public acceptance of genomics-related health information. OBJECTIVE: To explore how smokers come to accept or reject information about the relationship between genetics and nicotine addiction. METHODS: Thirteen focus groups (N = 84) were stratified by education (seven < Bachelor's degree, six ≥ Bachelor's degree) and race (eight black, five white). Participants viewed a 1-min video describing the discovery of a genetic variant associated with increased risk of nicotine addiction and lung cancer...
May 3, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28524895/scope-and-standards-defining-the-advanced-practice-role-in-genetics
#8
Alice S Kerber, Nancy J Ledbetter
Because knowledge concerning genetics and genomics and its application to oncology care is continuing to grow, oncology nurses must be aware of appropriate advanced scope of practice roles based on education and training. All nurses must develop and maintain knowledge of the field, but advanced practice nurses working in genetics have additional competencies and management expectations. Collaboration among practice levels and disciplines is essential. This article focuses on the advanced practice role as further defined in published resources outlining scope of practice in genetics...
June 1, 2017: Clinical Journal of Oncology Nursing
https://www.readbyqxmd.com/read/28524866/succession-in-the-petroleum-reservoir-microbiome-through-an-oil-field-production-lifecycle
#9
Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head, Nicolas Tsesmetzis
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28521789/a-comparative-evaluation-of-genome-assembly-reconciliation-tools
#10
Hind Alhakami, Hamid Mirebrahim, Stefano Lonardi
BACKGROUND: The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation...
May 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28521741/the-rainfall-plot-its-motivation-characteristics-and-pitfalls
#11
Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve
BACKGROUND: A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference genome, typically aiming to identify mutation hotspots. In general terms, the rainfall plot can be seen as a scatter plot showing the location of events on the x-axis versus the distance between consecutive events on the y-axis. Despite its frequent use, the motivation for applying this particular visualization and the appropriateness of its usage have never been critically addressed in detail...
May 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28521441/the-context-of-prostate-cancer-genomics-in-personalized-medicine
#12
Yanling Liu
Prostate cancer is one of the most common types of cancer in males. Heterogeneous genomic aberrations may lead to prostate cancer onset, progression and metastasis. This heterogeneity also contributes to the variety in cancer risk and outcomes, different drug responses and progression, observed between individual patients. Classical prognostic factors, including prostate-specific antigen, Gleason Score and clinical tumor staging, are not sufficient to portray the complexity of a clinically relevant cancer diagnosis, risk prognosis, treatment choice and therapy monitoring...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28517986/from-rosalind-franklin-to-barack-obama-data-sharing-challenges-and-solutions-in-genomics-and-personalised-medicine
#13
Mark Lawler, Tim Maughan
The collection, storage and use of genomic and clinical data from patients and healthy individuals is a key component of personalised medicine enterprises such as the Precision Medicine Initiative, the Cancer Moonshot and the 100,000 Genomes Project. In order to maximise the value of this data, it is important to embed a culture within the scientific, medical and patient communities that supports the appropriate sharing of genomic and clinical information. However, this aspiration raises a number of ethical, legal and regulatory challenges that need to be addressed...
April 2017: New Bioethics: a Multidisciplinary Journal of Biotechnology and the Body
https://www.readbyqxmd.com/read/28515774/complexity-and-algorithms-for-copy-number-evolution-problems
#14
Mohammed El-Kebir, Benjamin J Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
BACKGROUND: Cancer is an evolutionary process characterized by the accumulation of somatic mutations in a population of cells that form a tumor. One frequent type of mutations is copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome's copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis. RESULTS: We model the evolution of a tumor by segmental deletions and amplifications, and gauge distance from profile [Formula: see text] to [Formula: see text] by the minimum number of events needed to transform [Formula: see text] into [Formula: see text]...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28512461/transcriptional-responses-to-pre-flowering-leaf-defoliation-in-grapevine-berry-from-different-growing-sites-years-and-genotypes
#15
Sara Zenoni, Silvia Dal Santo, Giovanni B Tornielli, Erica D'Incà, Ilaria Filippetti, Chiara Pastore, Gianluca Allegro, Oriana Silvestroni, Vania Lanari, Antonino Pisciotta, Rosario Di Lorenzo, Alberto Palliotti, Sergio Tombesi, Matteo Gatti, Stefano Poni
Leaf removal is a grapevine canopy management technique widely used to modify the source-sink balance and/or microclimate around berry clusters to optimize fruit composition. In general, the removal of basal leaves before flowering reduces fruit set, hence achieving looser clusters, and improves grape composition since yield is generally curtailed more than proportionally to leaf area itself. Albeit responses to this practice seem quite consistent, overall vine performance is affected by genotype, environmental conditions, and severity of treatment...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28511612/ngs-analysis-on-tumor-tissue-and-cfdna-for-genotype-directed-therapy-in-metastatic-nsclc-patients-between-hope-and-hype
#16
Alexander T Falk, Simon Heeke, Véronique Hofman, Virginie Lespinet, Camille Ribeyre, Olivier Bordone, Michel Poudenx, Josiane Otto, Georges Garnier, Olivier Castelnau, Joël Guigay, Sylvie Leroy, Charles-Hugo Marquette, Paul Hofman, Marius Ilié
The advent of genomic based precision medicine led to the implementation of biomarker testing in metastatic non-small cell lung cancer (NSCLC) patients. Next generation sequencing (NGS) has been recently implemented to routine diagnostic requirements in lung oncology. Areas covered: Two cases of patients with metastatic NSCLC for whom NGS analysis performed on both tumor and liquid biopsy has not improved the clinical course of their disease are reported. These cases illustrate the difficulty of the so-called "personalized or precision" medicine in clinical routine practice for metastatic NSCLC...
May 17, 2017: Expert Review of Anticancer Therapy
https://www.readbyqxmd.com/read/28509679/the-impact-of-next-generation-sequencing-in-immunogenetics-current-status-and-future-directions
#17
Valia Bravo-Egana, Dimitri Monos
PURPOSE OF REVIEW: Next-generation sequencing (NGS) has now been established, and widely recognized, to be the preferred choice for human leukocyte antigen (HLA) typing. This transformation is based upon the many scientific, operational and economic benefits this technology affords. In this report, we review the major advantages, existing limitations and significant promise derived from adopting this technology in immunogenetics. RECENT FINDINGS: Significant benefits have emerged from the usage of NGS in a relatively short period, whereby we realize that this technology not only helps addressing the technical and operational problems we have had with the legacy methods for HLA typing, but equally important, it also allows for creative applications in stem cell and organ transplantation, new ways to investigate associations of the major histocompatibility complex (MHC) with many diseases and enhance our understanding regarding the MHC and non-MHC genomic interactions...
May 13, 2017: Current Opinion in Organ Transplantation
https://www.readbyqxmd.com/read/28508487/accuracy-of-genomic-breeding-values-revisited-assessment-of-two-established-approaches-and-a-novel-one-to-determine-the-accuracy-in-two-step-genomic-prediction
#18
G Ni, S Kipp, H Simianer, M Erbe
Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality. In previous studies, several methods were proposed to assess the accuracy of GBV including methods using population parameters or parameters inferred from mixed-model equations...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28508478/accuracy-of-genomic-within-family-selection-in-aquaculture-breeding-programmes
#19
M A Toro, M Saura, J Fernandez, B Villanueva
In aquaculture breeding programmes, selection within families cannot be applied for traits that cannot be recorded on the candidates (e.g., disease resistance or fillet quality). However, this problem can be overcome if genomic evaluation is used. Within-family genomic evaluation has been proposed for these programmes as large family sizes are available and substantial levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers even in populations in global linkage equilibrium...
June 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28505475/colorectal-cancer-subtypes-translation-to-routine-clinical-pathology
#20
REVIEW
Antonia K Roseweir, Donald C McMillan, Paul G Horgan, Joanne Edwards
Colorectal cancer (CRC) is the second most common cause of cancer death in Europe. Although outcomes have improved, it is clear that from a genomic standpoint CRC is not one disease, but a heterogeneous group of malignancies that arise within one organ. Given that different subtypes have different outcomes, the ability to subtype tumours in the clinic would be highly favourable, enabling optimal treatment for individual patients. In 2015, a consortium proposed four consensus subtypes for CRC (MSI immune, canonical, metabolic, and mesenchymal) based on six classifications systems reported to have prognostic value...
May 4, 2017: Cancer Treatment Reviews
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