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https://www.readbyqxmd.com/read/28435379/shifts-of-subgingival-bacterial-population-after-nonsurgical-and-pharmacological-therapy-of-localized-aggressive-periodontitis-followed-for-1-year-by-ion-torrent-pgm-platform
#1
Giuseppina Campisciano, Annamaria Toschetti, Manola Comar, Rosanna Di Taranto, Federico Berton, Claudio Stacchi
The possibility of targeting the hypervariable region V3 of the 16S rRNA gene using Ion Torrent Personal Genome Machine (PGM) could provide a complete analysis of subgingival plaque samples, potentially able to identify microbiological species missed by culture-based methods. A 16-year-old female smoker patient, affected by localized aggressive periodontitis, underwent a full-mouth disinfection protocol and was inserted in a 3-month recall program. Microbiological samples were collected at baseline and at 30, 100, 365 days follow-up and analyzed by Ion Torrent PGM...
January 2017: European Journal of Dentistry
https://www.readbyqxmd.com/read/28433457/spatial-and-temporal-expression-patterns-of-genes-around-nine-neuroticism-associated-loci
#2
Kazutaka Ohi, Takamitsu Shimada, Toshiki Yasuyama, Kohei Kimura, Takashi Uehara, Yasuhiro Kawasaki
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci...
April 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#3
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28429989/personalized-medicine-what-are-the-challenges-for-health-services
#4
Walter Ricciardi
Genetics and genomics, together with other biomedical sciences and digital technologies, have a vital role to play in transforming health services to become systems that can work for health in the 21st century in ways that are affordable and that respond to individuals' requirement for more autonomy. Health services should embrace this agenda and implement changes in the organization of care.
January 1, 2017: Journal of Health Services Research & Policy
https://www.readbyqxmd.com/read/28429075/toward-personalized-management-in-bladder-cancer-the-promise-of-novel-molecular-taxonomy
#5
REVIEW
Marie-Lisa Eich, Lars Dyrskjøt, George J Netto
Empowered by the recent advances in next generation sequencing and bioinformatics technology, an unprecedented wave of integrated transcriptomic and genomic studies have impacted the field of bladder cancer. These studies not only have confirmed previously charted genetic pathways in bladder cancer development but also have led to the discovery of numerous additional crucial driver genetic alterations. As a result, a novel genomic-based taxonomy is emerging that promises to better define clinically relevant intrinsic subtypes of bladder cancer...
April 21, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28429073/urinary-extracellular-vesicles-a-promising-shortcut-to-novel-biomarker-discoveries
#6
REVIEW
Karina Barreiro, Harry Holthofer
Proteomic and genomic techniques have reached full maturity and are providing unforeseen details for the comprehensive understanding of disease pathologies at a fraction of previous costs. However, for kidney diseases, many gaps in such information remain to inhibit major advances in the prevention, treatment and diagnostics of these devastating diseases, which have enormous global impact. The discovery of ubiquitous extracellular vesicles (EV) in all bodily fluids is rapidly increasing the fundamental knowledge of disease mechanisms and the ways in which cells communicate with distant locations in processes of cancer spread, immunological regulation, barrier functions and general modulation of cellular activity...
April 20, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28428977/19th-workshop-of-the-international-stroke-genetics-consortium-april-28-29-2016-boston-massachusetts-usa-2016-001-mri-defined-cerebrovascular-genomics-the-charge-consortium
#7
S Debette, Y Saba, D Vojinovic, X Jian, H Adams, G Chauhan, M Sargurupremraj, S Kaffashian, J Ding, J C Bis, P Nyquist, K Mather, C Van Duijn, L J Launer, M A Ikram, H Schmidt, W T Longstreth, M Fornage, S Seshadri
The CHARGE consortium is an investigator-initiated collaboration to facilitate meta-analyses of genome-wide association studies (GWAS) and genomic analyses based on next generation sequencing (NGS), among multiple large and well-phenotyped population-based cohort studies around the world (http://www.chargeconsortium.com). Within the neuro-CHARGE working group, we are presenting an update of ongoing genomic studies on MRI-markers of cerebrovascular disease. Large population-based studies have shown that the burden of cerebrovascular disease extends far beyond that of clinical stroke...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28428927/limitations-of-personalized-medicine-and-gene-assays-for-breast-cancer
#8
David Tiberi, Laura Masucci, Daniel Shedid, Isabelle Roy, Toni Vu, Erica Patocskai, André Robidoux, Philip Wong
Adjuvant systemic treatments reduce the risk of breast cancer recurrence following the local treatment of primary stage I-III breast cancers. For patients with hormone-positive breast cancers receiving hormonal therapy, the risk of distant recurrence is under 20% and therefore, many patients may potentially be spared of chemotherapy. Consequently, several molecular signatures based on gene expression were developed to better determine which breast cancer patients would benefit from chemotherapy. We present the case of a 62-year-old woman diagnosed with an early stage hormone receptor-positive breast cancer that was treated with a partial mastectomy...
March 17, 2017: Curēus
https://www.readbyqxmd.com/read/28424409/clinical-genomic-profiling-to-identify-actionable-alterations-for-investigational-therapies-in-patients-with-diverse-sarcomas
#9
Roman Groisberg, David S Hong, Vijaykumar Holla, Filip Janku, Sarina Piha-Paul, Vinod Ravi, Robert Benjamin, Shreyas Kumar Patel, Neeta Somaiah, Anthony Conley, Siraj M Ali, Alexa B Schrock, Jeffrey S Ross, Philip J Stephens, Vincent A Miller, Shiraj Sen, Cynthia Herzog, Funda Meric-Bernstam, Vivek Subbiah
BACKGROUND: There are currently no United States Food and Drug Administration approved molecularly matched therapies for sarcomas except gastrointestinal stromal tumors. Complicating this is the extreme diversity, heterogeneity, and rarity of these neoplasms. Few therapeutic options exist for relapsed and refractory sarcomas. In clinical practice many oncologists refer patients for genomic profiling hoping for guidance on treatment options after standard therapy. However, a systematic analysis of actionable mutations has yet to be completed...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423600/systematic-screening-of-isogenic-cancer-cells-identifies-dusp6-as-context-specific-synthetic-lethal-target-in-melanoma
#10
Stephanie Wittig-Blaich, Rainer Wittig, Steffen Schmidt, Stefan Lyer, Melanie Bewerunge-Hudler, Sabine Gronert-Sum, Olga Strobel-Freidekind, Carolin Müller, Markus List, Aleksandra Jaskot, Helle Christiansen, Mathias Hafner, Dirk Schadendorf, Ines Block, Jan Mollenhauer
Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies.We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423406/the-rise-of-radiomics-and-implications-for-oncologic-management
#11
Vivek Verma, Charles B Simone, Sunil Krishnan, Steven H Lin, Jinzhong Yang, Stephen M Hahn
Clinical medicine, particularly oncology, is progressing toward personalized care. Whereas the terms genomics, proteomics, transcriptomics, and metabolomics have dominated personalized medicine for the past couple decades, the concept of radiomics was first described in 2012. This nascent concept has major implications for personalized cancer care and involves extracting hundreds of standardized and quantifiable imaging characteristics from diagnostic computed tomography/magnetic resonance imaging images. The central hypothesis of radiomics is that these libraries of quantitative individual voxel-based variables are more sensitively associated with various clinical endpoints compared with the more qualitative radiologic, histopathologic, and clinical data more commonly utilized today...
July 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28418852/structural-homologies-between-phenformin-lipitor-and-gleevec-aim-the-same-metabolic-oncotarget-in-leukemia-and-melanoma
#12
REVIEW
Gábor Somlyai, T Que Collins, Emmanuelle J Meuillet, Patel Hitendra, Dominic P D'Agostino, László G Boros
Phenformin's recently demonstrated efficacy in melanoma and Gleevec's demonstrated anti-proliferative action in chronic myeloid leukemia may lie within these drugs' significant pharmacokinetics, pharmacodynamics and structural homologies, which are reviewed herein. Gleevec's success in turning a fatal leukemia into a manageable chronic disease has been trumpeted in medical, economic, political and social circles because it is considered the first successful targeted therapy. Investments have been immense in omics analyses and while in some cases they greatly helped the management of patients, in others targeted therapies failed to achieve clinically stable recurrence-free disease course or to substantially extend survival...
March 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418111/toward-the-dark-matter-of-natural-products
#13
REVIEW
Toshiyuki Wakimoto
Considering the dynamic features of natural products, our access toward exploring the entire diversity of natural products has been quite limited. It is challenging to assess the diversity of natural products by using conventional analytical methods, even with tandem chromatographic techniques, such as LC-MS and GC-MS. This viewpoint is supported by the sequencing analyses of microbial genomes, which have unveiled the potential of secondary metabolite production far exceeding the number of isolated molecules...
April 18, 2017: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/28416894/letter-to-the-editor-a-genetic-based-algorithm-for-personalized-resistance-training
#14
A Karanikolou, G Wang, Y Pitsiladis
In a recent paper entitled "A genetic-based algorithm for personalized resistance training", Jones et al. [1] presented an algorithm of 15 performance-associated gene polymorphisms that they propose can determine an athlete's training response by predicting power and endurance potential. However, from the design of their studies and the data provided, there is no evidence to support these authors' assertions. Progress towards such a significant development in the field of sport and exercise genomics will require a paradigm shift in line with recent recommendations for international collaborations such as the Athlome Project (see www...
March 2017: Biology of Sport
https://www.readbyqxmd.com/read/28415856/gene-and-variant-annotation-for-mendelian-disorders-in-the-era-of-advanced-sequencing-technologies
#15
Samya Chakravorty, Madhuri Hegde
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations...
April 17, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28415835/the-role-of-chemotherapy-in-unresectable-or-metastatic-adenocarcinoma-of-the-stomach-and-gastroesophageal-junction
#16
Mustafa Bozkurt, Fatemeh G Amlashi, Mariela Blum Murphy
Gastric cancer including gastro-esophageal junction adenocarcinomas are most challenging and deadly cancers of the gastrointestinal tract. Gastric cancer has a fatality-to-case ratio of 0.66, translating that nearly two thirds of newly diagnosed patients will have disseminated disease and in need of systemic therapy (1). Advanced gastric adenocarcinoma (AGC) is a heterogenous disease with differences in geographical distribution, histopathology, and molecular subtypes. Fluoropyrimidines (5-FU, S-1, and capecitabine), platinum compounds (cisplatin, oxaliplatin), taxanes (paclitaxel, docetaxel), and the topoisomerase inhibitory irinotecan are active drugs against AGC...
April 14, 2017: Minerva Chirurgica
https://www.readbyqxmd.com/read/28415743/survival-differences-of-cimp-subtypes-integrated-with-cna-information-in-human-breast-cancer
#17
Huihan Wang, Weili Yan, Shumei Zhang, Yue Gu, Yihan Wang, Yanjun Wei, Hongbo Liu, Fang Wang, Qiong Wu, Yan Zhang
CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation...
March 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415679/a-feasibility-study-of-returning-clinically-actionable-somatic-genomic-alterations-identified-in-a-research-laboratory
#18
Natalia Paez Arango, Lauren Brusco, Kenna R Mills Shaw, Ken Chen, Agda Karina Eterovic, Vijaykumar Holla, Amber Johnson, Beate Litzenburger, Yekaterina B Khotskaya, Nora Sanchez, Ann Bailey, Xiaofeng Zheng, Chacha Horombe, Scott Kopetz, Carol J Farhangfar, Mark Routbort, Russell Broaddus, Elmer V Bernstam, John Mendelsohn, Gordon B Mills, Funda Meric-Bernstam
PURPOSE: Molecular profiling performed in the research setting usually does not benefit the patients that donate their tissues. Through a prospective protocol, we sought to determine the feasibility and utility of performing broad genomic testing in the research laboratory for discovery, and the utility of giving treating physicians access to research data, with the option of validating actionable alterations in the CLIA environment. EXPERIMENTAL DESIGN: 1200 patients with advanced cancer underwent characterization of their tumors with high depth hybrid capture sequencing of 201 genes in the research setting...
March 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28413712/variation-within-mbp-gene-predicts-disease-course-in-multiple-sclerosis
#19
Yuan Zhou, Steve Simpson, Jac C Charlesworth, Ingrid van der Mei, Robyn M Lucas, Anne-Louise Ponsonby, Bruce V Taylor
OBJECTIVE: Prognosis following a first demyelinating event is difficult to predict, with no genetic markers of MS progression currently identified. Myelin basic protein (MBP) is a major component of the myelin sheath of CNS neurons and may play a central role in demyelinating diseases such as MS. However, genetic variation in MBP has not been implicated in MS onset risk in large genome-wide association studies. We hypothesized that genetic variations in MBP may be a determinant of MS clinical course...
April 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28412930/large-scale-analysis-of-post-translational-modifications-in-e-coli-under-glucose-limiting-conditions
#20
Colin W Brown, Viswanadham Sridhara, Daniel R Boutz, Maria D Person, Edward M Marcotte, Jeffrey E Barrick, Claus O Wilke
BACKGROUND: Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects...
April 17, 2017: BMC Genomics
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