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Medical genomics

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https://www.readbyqxmd.com/read/29334348/assessing-the-readiness-of-precision-medicine-interoperabilty-an-exploratory-study-of-the-national-institutes-of-health-genetic-testing-registry
#1
Jay G Ronquillo, Chunhua Weng, William T Lester
BACKGROUND:   Precision medicine involves three major innovations currently taking place in healthcare:  electronic health records, genomics, and big data.  A major challenge for healthcare providers, however, is understanding the readiness for practical application of initiatives like precision medicine. OBJECTIVE:   To better understand the current state and challenges of precision medicine interoperability using a national genetic testing registry as a starting point, placed in the context of established interoperability formats...
November 17, 2017: Journal of Innovation in Health Informatics
https://www.readbyqxmd.com/read/29334346/in-this-issue-prerequisites-for-precision-medicine-are-genomics-computerised-medical-record-systems-and-big-data-analytics
#2
Simon De Lusignan
No abstract text is available yet for this article.
January 12, 2018: Journal of Innovation in Health Informatics
https://www.readbyqxmd.com/read/29331453/are-privacy-enhancing-technologies-for-genomic-data-ready-for-the-clinic-a-survey-of-medical-experts-of-the-swiss-hiv-cohort-study
#3
Jean-Louis Raisaro, Paul J McLaren, Jacques Fellay, Matthias Cavassini, Catherine Klersy, Jean-Pierre Hubaux
PURPOSE: Protecting patient privacy is a major obstacle for the implementation of genomic-based medicine. Emerging privacy-enhancing technologies can become key enablers for managing sensitive genetic data. We studied physicians' attitude toward this kind of technology in order to derive insights that might foster their future adoption for clinical care. METHODS: We conducted a questionnaire-based survey among 55 physicians of the Swiss HIV Cohort Study who tested the first implementation of a privacy-preserving model for delivering genomic test results...
January 10, 2018: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29330528/application-of-weighted-gene-co-expression-network-analysis-for-data-from-paired-design
#4
Jianqiang Li, Doudou Zhou, Weiliang Qiu, Yuliang Shi, Ji-Jiang Yang, Shi Chen, Qing Wang, Hui Pan
Investigating how genes jointly affect complex human diseases is important, yet challenging. The network approach (e.g., weighted gene co-expression network analysis (WGCNA)) is a powerful tool. However, genomic data usually contain substantial batch effects, which could mask true genomic signals. Paired design is a powerful tool that can reduce batch effects. However, it is currently unclear how to appropriately apply WGCNA to genomic data from paired design. In this paper, we modified the current WGCNA pipeline to analyse high-throughput genomic data from paired design...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330025/the-role-of-extracellular-and-intracellular-nicotinamide-phosphoribosyl-transferase-in-cancer-diagnostic-and-therapeutic-perspectives-and-challenges
#5
REVIEW
Maria Dalamaga, Gerasimos Socrates Christodoulatos, Christos S Mantzoros
Nicotinamide phosphoribosyl-transferase (Nampt) or pre-B cell colony-enhancing factor or visfatin represents a pleiotropic molecule acting as an enzyme, a cytokine and a growth factor. Intracellular Nampt plays an important role in cellular bioenergetics and metabolism, particularly NAD biosynthesis. NAD biosynthesis is critical in DNA repair, oncogenic signal transduction, transcription, genomic integrity and apoptosis. Although its insulin-mimetic function remains a controversial issue, extracellular Nampt presents proliferative, anti-apoptotic, pro-inflammatory, pro-angiogenic and metastatic properties...
January 9, 2018: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/29329601/nicotiana-glauca-whole-genome-investigation-for-ct-dna-study
#6
Galina Khafizova, Pavel Dobrynin, Dmitrii Polev, Tatiana Matveeva
OBJECTIVE: Nicotiana glauca (tree tobacco) is a naturally transgenic plant, containing sequences acquired from Agrobacterium rhizogenes by horizontal gene transfer. Besides, N. glauca contains a wide profile of alkaloids of medical interest. DATA DESCRIPTION: We report a high-depth sequencing and de novo assembly of N. glauca full genome and analysis of genome elements with bacterial origin. The draft genome assembly is 3.2 Gb, with N50 size of 31.1 kbp. Comparative analysis confirmed the presence of single, previously described gT insertion...
January 12, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29326013/a-cluster-of-multidrug-resistant-mycobacterium-tuberculosis-among-patients-arriving-in-europe-from-the-horn-of-africa-a-molecular-epidemiological-study
#7
Timothy M Walker, Matthias Merker, Astrid M Knoblauch, Peter Helbling, Otto D Schoch, Marieke J van der Werf, Katharina Kranzer, Lena Fiebig, Stefan Kröger, Walter Haas, Harald Hoffmann, Alexander Indra, Adrian Egli, Daniela M Cirillo, Jérôme Robert, Thomas R Rogers, Ramona Groenheit, Anne T Mengshoel, Vanessa Mathys, Marjo Haanperä, Dick van Soolingen, Stefan Niemann, Erik C Böttger, Peter M Keller
BACKGROUND: The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. METHODS: On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis...
January 8, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29325607/genetic-and-genomic-testing-for-neurologic-disease-in-clinical-practice
#8
Brent L Fogel
The influence of genetics on neurologic disease is broad and it is becoming more common that clinicians are presented with a patient whose disease is likely of genetic origin. In the search for mutations causing Mendelian disorders, advances in genetic testing methodology have propelled modern neurologic practice beyond single-gene testing into the realm of genomic medicine, where routine evaluations encompass hundreds or thousands of genes, or even the entire exome, representing all protein-coding genes in the genome...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325267/-analysis-of-clinical-outcomes-of-different-embryo-stage-biopsy-in-array-comparative-genomic-hybridization-based-preimplantation-genetic-diagnosis-and-screening
#9
J D Shen, W Wu, L Shu, L L Cai, J Z Xie, L Ma, X P Sun, Y G Cui, J Y Liu
Objective: To evaluate the efficiency of the application of array comparative genomic hybridization (array-CGH) in preimplantation genetic diagnosis or screening (PGD/PGS), and compare the clinical outcomes of different stage embryo biopsy. Methods: The outcomes of 381 PGD/PGS cycles referred in the First Affiliated Hospital of Nanjing Medical University from July 2011 to August 2015 were retrospectively analyzed. There were 320 PGD cycles with 156 cleavage-stage-biopsy cycles and 164 trophectoderm-biopsy cycles, 61 PGS cycles with 23 cleavage-stage-biopsy cycles and 38 trophectoderm-biopsy cycles...
December 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/29324852/real-life-helping-behaviours-in-north-america-a-genome-wide-association-approach
#10
Georg Primes, Martin Fieder
In humans, prosocial behaviour is essential for social functioning. Twin studies suggest this distinct human trait to be partly hardwired. In the last decade research on the genetics of prosocial behaviour focused on neurotransmitters and neuropeptides, such as oxytocin, dopamine, and their respective pathways. Recent trends towards large scale medical studies targeting the genetic basis of complex diseases such as Alzheimer's disease and schizophrenia pave the way for new directions also in behavioural genetics...
2018: PloS One
https://www.readbyqxmd.com/read/29323820/genetics-and-genomics-in-clinical-practice-the-views-of-wisconsin-physicians
#11
Michael P McCauley, Rebecca K Marcus, Kimberly A Strong, Alexis M Visotcky, Mary E Shimoyama, Arthur R Derse
INTRODUCTION: Decreasing costs and increased availability of genetic testing and genome sequencing mean many physicians will consider using these services over the next few years. Despite this promising future, some argue the present roadmap for translating genetics and genomics into routine clinical practice is unclear. OBJECTIVE: We conducted a pilot study to explore Wisconsin physicians' views, practices and educational desires regarding genetic and genomic testing...
June 2017: WMJ: Official Publication of the State Medical Society of Wisconsin
https://www.readbyqxmd.com/read/29323668/professional-responsibilities-regarding-the-provision-publication-and-dissemination-of-patient-phenotypes-in-the-context-of-clinical-genetic-and-genomic-testing-points-to-consider-a-statement-of-the-american-college-of-medical-genetics-and-genomics-acmg
#12
Lynn W Bush, Anita E Beck, Leslie G Biesecker, James P Evans, Ada Hamosh, Ingrid A Holm, Christa L Martin, C Sue Richards, Heidi L Rehm
Disclaimer: This Points to Consider document is designed as an educational resource to provide best practices for medical genetic clinicians, laboratories, and journals regarding the provision, publication, and dissemination of patient phenotypes in the context of genomic testing, clinical genetic practice, and research. While the goal of the document is the improvement of patient care, the considerations and practices described should not be considered inclusive of all proper considerations and practices or exclusive of others that are reasonably directed to obtaining the same goal...
January 11, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29322937/predicting-binary-discrete-and-continued-lncrna-disease-associations-via-a-unified-framework-based-on-graph-regression
#13
Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Yu-Xi Long, Siu-Ming Yiu
BACKGROUND: In human genomes, long non-coding RNAs (lncRNAs) have attracted more and more attention because their dysfunctions are involved in many diseases. However, the associations between lncRNAs and diseases (LDA) still remain unknown in most cases. While identifying disease-related lncRNAs in vivo is costly, computational approaches are promising to not only accelerate the possible identification of associations but also provide clues on the underlying mechanism of various lncRNA-caused diseases...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29321635/pan-genome-analysis-of-the-genus-finegoldia-identifies-two-distinct-clades-strain-specific-heterogeneity-and-putative-virulence-factors
#14
Holger Brüggemann, Anders Jensen, Seven Nazipi, Hüsnü Aslan, Rikke Louise Meyer, Anja Poehlein, Elzbieta Brzuszkiewicz, Munir A Al-Zeer, Volker Brinkmann, Bo Söderquist
Finegoldia magna, a Gram-positive anaerobic coccus, is an opportunistic pathogen, associated with medical device-related infections. F. magna is the only described species of the genus Finegoldia. We report the analysis of 17 genomes of Finegoldia isolates. Phylogenomic analyses showed that the Finegoldia population can be divided into two distinct clades, with an average nucleotide identity of 90.7%. One clade contains strains of F. magna, whereas the other clade includes more heterogeneous strains, hereafter tentatively named "Finegoldia nericia"...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29316365/developing-pharmacogenomic-reports-insights-from-patients-and-clinicians
#15
Laney K Jones, Alanna Kulchak Rahm, Michael R Gionfriddo, Janet L Williams, Audrey L Fan, Rebecca A Pulk, Eric A Wright, Marc S Williams
Increasingly, for a variety of indications, patients have their genomes sequenced and actionable results returned. A subset of returned results is pharmacogenomic (PGx) variants involved in the metabolism or action of medications. Although the impact of these variants on health is well-documented, little research exists on how to communicate these findings to patients and clinicians. We conducted semistructured interviews with end users to understand how best to communicate PGx results. Overall, patients and clinicians had similar opinions regarding report content, delivery, and application...
January 8, 2018: Clinical and Translational Science
https://www.readbyqxmd.com/read/29315417/interactive-or-static-reports-to-guide-clinical-interpretation-of-cancer-genomics
#16
Stacy W Gray, Jeffrey Gagan, Ethan Cerami, Angel M Cronin, Hajime Uno, Nelly Oliver, Carol Lowenstein, Ruth Lederman, Anna Revette, Aaron Suarez, Charlotte Lee, Jordan Bryan, Lynette Sholl, Eliezer M Van Allen
Objective: Misinterpretation of complex genomic data presents a major challenge in the implementation of precision oncology. We sought to determine whether interactive genomic reports with embedded clinician education and optimized data visualization improved genomic data interpretation. Materials and Methods: We conducted a randomized, vignette-based survey study to determine whether exposure to interactive reports for a somatic gene panel, as compared to static reports, improves physicians' genomic comprehension and report-related satisfaction (overall scores calculated across 3 vignettes, range 0-18 and 1-4, respectively, higher score corresponding with improved endpoints)...
January 5, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29314583/novel-mutations-and-phenotypes-of-epilepsy-associated-genes-in-epileptic-encephalopathies
#17
Peng Zhou, Na He, Jing-Wen Zhang, Zhi-Jian Lin, Jie Wang, Li-Min Yan, Heng Meng, Bin Tang, Bing-Mei Li, Xiao-Rong Liu, Yi-Wu Shi, Qiong-Xiang Zhai, Yong-Hong Yi, Wei-Ping Liao
Epileptic encephalopathies are severe epilepsy disorders with strong genetic bases. We performed targeted next-generation sequencing in 70 patients with epileptic encephalopathies. The likely pathogenicity of variants in candidate genes was evaluated by American College of Medical Genetics and Genomics (ACMG) scoring taken together with the accepted clinical presentation. Thirty-three candidate variants were detected after population filtration and computational prediction. According to ACMG, 21 candidate variants, including 18 de novo variants, were assessed to be pathogenic/likely pathogenic with clinical concordance...
January 4, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29313404/vitamin-d-diminishes-the-high-platelet-aggregation-of-type-2-diabetes-mellitus-patients
#18
Maya Sultan, Orit Twito, Tali Tohami, Erez Ramati, Eran Neumark, Gloria Rashid
Platelet activation is found in inflammatory conditions and implicated in the pathogenesis of chronic medical conditions, such as atherosclerosis, coronary vascular disease, cerebrovascular disease, and diabetes mellitus (DM). HbA1c is inversely related to vitamin D25 levels in individuals with and without DM. This study aimed to determine the relation between platelet aggregation, vitamin D and HbA1c among healthy individuals and those with Type 2 DM (T2DM). The direct effect of vitamin D1, 25 (calcitriol) on platelet aggregation was also investigated...
January 9, 2018: Platelets
https://www.readbyqxmd.com/read/29311563/ensemble-landmarking-of-3d-facial-surface-scans
#19
Markus A de Jong, Pirro Hysi, Tim Spector, Wiro Niessen, Maarten J Koudstaal, Eppo B Wolvius, Manfred Kayser, Stefan Böhringer
Landmarking of 3D facial surface scans is an important analysis step in medical and biological applications, such as genome-wide association studies (GWAS). Manual landmarking is often employed with considerable cost and rater dependent variability. Landmarking automatically with minimal training is therefore desirable. We apply statistical ensemble methods to improve automated landmarking of 3D facial surface scans. Base landmarking algorithms using features derived from 3D surface scans are combined using either bagging or stacking...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29310515/persons-with-chronic-spinal-cord-injury-have-decreased-nk-cell-and-increased-tlr-inflammatory-gene-expression
#20
Paige Herman, Adam B Stein, Katie Gibbs, Ilya Korsunsky, Peter Gregersen, Ona Bloom
Infections are the leading cause of death for individuals with traumatic spinal cord injury (SCI). Along with increased infection rates, inflammation is often also observed in persons with chronic SCI. Together, immunological changes after SCI are also poised to impede neurological recovery and to mediate common medical consequences of SCI, including atherogenesis and neuropathic pain. The molecular mechanisms contributing to increased infection susceptibility and inflammation in persons living with SCI are poorly understood...
January 8, 2018: Journal of Neurotrauma
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