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https://www.readbyqxmd.com/read/28212969/lessons-learned-when-introducing-pharmacogenomic-panel-testing-into-clinical-practice
#1
Marc B Rosenman, Brian Decker, Kenneth D Levy, Ann M Holmes, Victoria M Pratt, Michael T Eadon
OBJECTIVES: Implementing new programs to support precision medicine in clinical settings is a complex endeavor. We describe challenges and potential solutions based on the Indiana GENomics Implementation: an Opportunity for the Underserved (INGenious) program at Eskenazi Health-one of six sites supported by the Implementing GeNomics In pracTicE network grant of the National Institutes of Health/National Human Genome Research Institute. INGenious is an implementation of a panel of genomic tests...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212287/big-data-analytics-for-genomic-medicine
#2
REVIEW
Karen Y He, Dongliang Ge, Max M He
Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28209747/pediatric-adolescent-and-young-adult-thyroid-carcinoma-harbors-frequent-and-diverse-targetable-genomic-alterations-including-kinase-fusions
#3
Pierre Vanden Borre, Alexa B Schrock, Peter M Anderson, John C Morris, Andreas M Heilmann, Oliver Holmes, Kai Wang, Adrienne Johnson, Steven G Waguespack, Sai-Hong Ignatius Ou, Saad Khan, Kar-Ming Fung, Philip J Stephens, Rachel L Erlich, Vincent A Miller, Jeffrey S Ross, Siraj M Ali
BACKGROUND: Thyroid carcinoma, which is rare in pediatric patients (age 0-18 years) but more common in adolescent and young adult (AYA) patients (age 15-39 years), carries the potential for morbidity and mortality. METHODS: Hybrid-capture-based comprehensive genomic profiling (CGP) was performed prospectively on 512 consecutively submitted thyroid carcinomas, including 58 from pediatric and AYA (PAYA) patients, to identify genomic alterations (GAs), including base substitutions, insertions/deletions, copy number alterations, and rearrangements...
February 16, 2017: Oncologist
https://www.readbyqxmd.com/read/28207434/leveraging-information-from-genetic-risk-scores-of-coronary-atherosclerosis
#4
Themistocles L Assimes, Elias L Salfati, Liana C Del Gobbo
PURPOSE OF REVIEW: Genome-wide association studies (GWAS) have identified ∼60 loci for coronary artery disease (CAD). Through genetic risk scores (GRSs), investigators are leveraging this genomic information to gain insights on both the fundamental mechanisms driving these associations as well as their utility in improving risk prediction. RECENT FINDINGS: GRSs of CAD track with the earliest atherosclerosis lesions in the coronary including fatty streaks and uncomplicated raised lesions...
February 14, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28207198/integrated-precision-medicine-the-role-of-electronic-health-records-in-delivering-personalized-treatment
#5
REVIEW
Amy Sitapati, Hyeoneui Kim, Barbara Berkovich, Rebecca Marmor, Siddharth Singh, Robert El-Kareh, Brian Clay, Lucila Ohno-Machado
Precision Medicine involves the delivery of a targeted, personalized treatment for a given patient. By harnessing the power of electronic health records (EHRs), we are increasingly able to practice precision medicine to improve patient outcomes. In this article, we introduce the scientific community at large to important building blocks for personalized treatment, such as terminology standards that are the foundation of the EHR and allow for exchange of health information across systems. We briefly review different types of clinical decision support (CDS) and present the current state of CDS, which is already improving the care patients receive with genetic profile-based tailored recommendations regarding diagnostic and treatment plans...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28205241/septic-transfusion-case-caused-by-a-platelet-pool-with-visible-clotting-due-to-contamination-with-staphylococcus-aureus
#6
Maria Loza-Correa, Yuntong Kou, Mariam Taha, Miloslav Kalab, Jennifer Ronholm, Patrick M Schlievert, Michael P Cahill, Robert Skeate, Christine Cserti-Gazdewich, Sandra Ramirez-Arcos
BACKGROUND: Contamination of platelet concentrates (PCs) with Staphylococcus aureus is one of the most significant ongoing transfusion safety risks in developed countries. CASE REPORT: This report describes a transfusion reaction in an elderly patient diagnosed with acute myeloid leukemia, transfused with a 4-day-old buffy coat PC through a central venous catheter. The transfusion was interrupted when a large fibrous clot in the PC obstructed infusion pump flow...
February 16, 2017: Transfusion
https://www.readbyqxmd.com/read/28202904/genome-wide-dna-de-methylation-is-associated-with-noninfectious-bud-failure-exhibition-in-almond-prunus-dulcis-mill-d-a-webb
#7
Jonathan Fresnedo-Ramírez, Helen M Chan, Dan E Parfitt, Carlos H Crisosto, Thomas M Gradziel
Noninfectious bud-failure (BF) remains a major threat to almond production in California, particularly with the recent rapid expansion of acreage and as more intensive cultural practices and modern cultivars are adopted. BF has been shown to be inherited in both vegetative and sexual progeny, with exhibition related to the age and propagation history of scion clonal sources. These characteristics suggest an epigenetic influence, such as the loss of juvenility mediated by DNA-(de)methylation. Various degrees of BF have been reported among cultivars as well as within sources of clonal propagation of the same cultivar...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28201946/sorting-permutations-by-prefix-and-suffix-rearrangements
#8
Carla Negri Lintzmayer, Guillaume Fertin, Zanoni Dias
Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations...
February 9, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28199897/real-world-utility-of-whole-exome-sequencing-with-targeted-gene-analysis-for-focal-epilepsy
#9
Piero Perucca, Ingrid E Scheffer, A Simon Harvey, Paul A James, Sebastian Lunke, Natalie Thorne, Clara Gaff, Brigid M Regan, John A Damiano, Michael S Hildebrand, Samuel F Berkovic, Terence J O'Brien, Patrick Kwan
OBJECTIVE: Driven by advances in genomic technology and reduction in costs, next-generation sequencing (NGS) is venturing into routine clinical care. The 'real-world' clinical utility of NGS remains to be determined in focal epilepsies, which account for 60% of all epilepsies and for which the importance of genetic factors is just beginning to emerge. We investigated the diagnostic yield and management implications of whole exome sequencing (WES)-based screening of selected genes in the routine care of common focal epilepsies suspected to have a genetic basis...
February 7, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28198679/detecting-discordance-enrichment-among-a-series-of-two-sample-genome-wide-expression-data-sets
#10
Yinglei Lai, Fanni Zhang, Tapan K Nayak, Reza Modarres, Norman H Lee, Timothy A McCaffrey
BACKGROUND: With the current microarray and RNA-seq technologies, two-sample genome-wide expression data have been widely collected in biological and medical studies. The related differential expression analysis and gene set enrichment analysis have been frequently conducted. Integrative analysis can be conducted when multiple data sets are available. In practice, discordant molecular behaviors among a series of data sets can be of biological and clinical interest. METHODS: In this study, a statistical method is proposed for detecting discordance gene set enrichment...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196726/use-of-genome-sequencing-to-identify-hepatitis-c-virus-transmission-in-a-renal-healthcare-setting
#11
M I Garvey, C W Bradley, K L Holden, P Hewins, S-L Ngui, R Tedder, P Jumaa, E Smit
Hepatitis C virus (HCV) infection is a major health burden worldwide. A patient with no history of HCV infection while on a renal unit was found to seroconvert to HCV. Here we report the use of sequencing to postulate how transmission of HCV occurred in a healthcare setting, and how this guided our outbreak investigation. Based on infection control inspections the transmission event was surmised to be due to ward environmental contamination with blood and subsequent inoculation from intravenous interventions on the patient acquiring HCV...
January 16, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28196593/liquid-biopsies-what-we-do-not-know-yet
#12
REVIEW
Alberto Bardelli, Klaus Pantel
The inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens. Analysis of cell-free DNA and circulating tumor cells has the potential to change clinical practice by exploiting blood rather than tissue as a source of information. Liquid biopsies are already used to monitor disease response and track the emergence of drug resistance. The suitability of blood-based molecular profiles for early detection and monitoring minimal residual disease is being evaluated...
February 13, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28193735/comprehensive-genomic-profiling-aids-in-distinguishing-metastatic-recurrence-from-second-primary-cancers
#13
Benjamin A Weinberg, Kyle Gowen, Thomas K Lee, Sai-Hong Ignatius Ou, Robert Bristow, Lauren Krill, M Isabel Almira-Suarez, Siraj M Ali, Vincent A Miller, Stephen V Liu, Samuel J Klempner
BACKGROUND: Metastatic recurrence after treatment for locoregional cancer is a major cause of morbidity and cancer-specific mortality. Distinguishing metastatic recurrence from the development of a second primary cancer has important prognostic and therapeutic value and represents a difficult clinical scenario. Advances beyond histopathological comparison are needed. We sought to interrogate the ability of comprehensive genomic profiling (CGP) to aid in distinguishing between these clinical scenarios...
February 13, 2017: Oncologist
https://www.readbyqxmd.com/read/28193464/igas-a-framework-for-using-electronic-intraoperative-medical-records-for-genomic-discovery
#14
Matthew A Levin, Thomas T Joseph, Janina M Jeff, Rajiv Nadukuru, Stephen B Ellis, Erwin P Bottinger, Eimear E Kenny
OBJECTIVE: Design and implement a HIPAA and Integrating the Healthcare Enterprise (IHE) profile compliant automated pipeline, the integrated Genomics Anesthesia System (iGAS), linking genomic data from the Mount Sinai Health System (MSHS) BioMe biobank to electronic anesthesia records, including physiological data collected during the perioperative period. The resulting repository of multi-dimensional data can be used for precision medicine analysis of physiological readouts, acute medical conditions, and adverse events that can occur during surgery...
February 10, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28192596/integrating-next-generation-sequencing-into-pediatric-oncology-practice-an-assessment-of-physician-confidence-and-understanding-of-clinical-genomics
#15
Liza-Marie Johnson, Jessica M Valdez, Emily A Quinn, April D Sykes, Rose B McGee, Regina Nuccio, Stacy J Hines-Dowell, Justin N Baker, Chimene Kesserwan, Kim E Nichols, Belinda N Mandrell
BACKGROUND: The incorporation of genomic testing to identify targetable somatic alterations and predisposing germline mutations into the clinical setting is becoming increasingly more common. Despite its potential usefulness, to the authors' knowledge physician confidence with regard to understanding and applying genomic testing remains unclear, particularly within the realm of pediatric oncology. METHODS: Before initiating an institutional feasibility study regarding the integration of clinical genomic testing, the authors surveyed pediatric oncologists regarding their confidence around understanding of genomic testing, perceived usefulness of test results, preferences around the disclosure of germline test results, and possible risks and benefits of testing...
February 13, 2017: Cancer
https://www.readbyqxmd.com/read/28191760/directing-differentiation-of-pluripotent-stem-cells-toward-retinal-pigment-epithelium-lineage
#16
Parul Choudhary, Heather Booth, Alex Gutteridge, Beata Surmacz, Irene Louca, Juliette Steer, Julie Kerby, Paul John Whiting
Development of efficient and reproducible conditions for directed differentiation of pluripotent stem cells into specific cell types is important not only to understand early human development but also to enable more practical applications, such as in vitro disease modeling, drug discovery, and cell therapies. The differentiation of stem cells to retinal pigment epithelium (RPE) in particular holds promise as a source of cells for therapeutic replacement in age-related macular degeneration. Here we show development of an efficient method for deriving homogeneous RPE populations in a period of 45 days using an adherent, monolayer system and defined xeno-free media and matrices...
February 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28190876/the-evolution-of-tumour-phylogenetics-principles-and-practice
#17
REVIEW
Russell Schwartz, Alejandro A Schäffer
Rapid advances in high-throughput sequencing and a growing realization of the importance of evolutionary theory to cancer genomics have led to a proliferation of phylogenetic studies of tumour progression. These studies have yielded not only new insights but also a plethora of experimental approaches, sometimes reaching conflicting or poorly supported conclusions. Here, we consider this body of work in light of the key computational principles underpinning phylogenetic inference, with the goal of providing practical guidance on the design and analysis of scientifically rigorous tumour phylogeny studies...
February 13, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28188908/hive-heptagon-a-sensible-variant-calling-algorithm-with-post-alignment-quality-controls
#18
Vahan Simonyan, Konstantin Chumakov, Eric Donaldson, Konstantinos Karagiannis, Phuc VinhNguyen Lam, Hayley Dingerdissen, Alin Voskanian
: Advances in high-throughput sequencing (HTS) technologies have greatly increased the availability of genomic data and potential discovery of clinically significant genomic variants. However, numerous issues still exist with the analysis of these data, including data complexity, the absence of formally agreed upon best practices, and inconsistent reproducibility. Toward a more robust and reproducible variant-calling paradigm, we propose a series of selective noise filtrations and post-alignment quality control (QC) techniques that may reduce the rate of false variant calls...
February 7, 2017: Genomics
https://www.readbyqxmd.com/read/28186864/within-day-baseline-variation-in-salivary-biomarkers-in-healthy-men
#19
Firman Prathama Idris, Yunxia Wan, Xi Zhang, Chamindie Punyadeera
Saliva is an easily accessible sample and offers practical and noninvasive biomarker solutions as an alternative to blood and urine-based diagnostics. Saliva contains a plethora of biomolecules such as nucleic acids, hormones, proteins, and electrolytes. On the other hand, little is known on the extent to which the biomolecules in saliva vary over time within a given person. This baseline information is crucial for future development of robust saliva-based diagnostics. We have collected unstimulated whole mouth saliva from 20 healthy young men at four times during the day, including before and after a meal...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28185578/fast-ancestral-gene-order-reconstruction-of-genomes-with-unequal-gene-content
#20
Pedro Feijão, Eloi Araujo
BACKGROUND: During evolution, genomes are modified by large scale structural events, such as rearrangements, deletions or insertions of large blocks of DNA. Of particular interest, in order to better understand how this type of genomic evolution happens, is the reconstruction of ancestral genomes, given a phylogenetic tree with extant genomes at its leaves. One way of solving this problem is to assume a rearrangement model, such as Double Cut and Join (DCJ), and find a set of ancestral genomes that minimizes the number of events on the input tree...
November 11, 2016: BMC Bioinformatics
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