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Clinical omics

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https://www.readbyqxmd.com/read/28436686/sparking-thinking-studying-modern-precision-medicine-will-accelerate-the-progression-of-traditional-chinese-medicine-patterns
#1
Bao-Cheng Liu, Guang Ji
Incorporating "-omics" studies with environmental interactions could help elucidate the biological mechanisms responsible for Traditional Chinese Medicine (TCM) patterns. Based on the authors' own experiences, this review outlines a model of an ideal combination of "-omics" biomarkers, environmental factors, and TCM pattern classifications; provides a narrative review of the relevant genetic and TCM studies; and lists several successful integrative examples. Two integration tools are briefly introduced. The first is the integration of modern devices into objective diagnostic methods of TCM patterning, which would improve current clinical decision-making and practice...
April 24, 2017: Journal of Alternative and Complementary Medicine: Research on Paradigm, Practice, and Policy
https://www.readbyqxmd.com/read/28435157/the-systemic-nature-of-ckd
#2
REVIEW
Carmine Zoccali, Raymond Vanholder, Ziad A Massy, Alberto Ortiz, Pantelis Sarafidis, Friedo W Dekker, Danilo Fliser, Denis Fouque, Gunnar H Heine, Kitty J Jager, Mehmet Kanbay, Francesca Mallamaci, Gianfranco Parati, Patrick Rossignol, Andrzej Wiecek, Gerard London
The accurate definition and staging of chronic kidney disease (CKD) is one of the major achievements of modern nephrology. Intensive research is now being undertaken to unravel the risk factors and pathophysiologic underpinnings of this disease. In particular, the relationships between the kidney and other organs have been comprehensively investigated in experimental and clinical studies in the last two decades. Owing to technological and analytical limitations, these links have been studied with a reductionist approach focusing on two organs at a time, such as the heart and the kidney or the bone and the kidney...
April 24, 2017: Nature Reviews. Nephrology
https://www.readbyqxmd.com/read/28423769/linked-data-applications-through-ontology-based-data-access-in-clinical-research
#3
Ann-Kristin Kock-Schoppenhauer, Christian Kamann, Hannes Ulrich, Petra Duhm-Harbeck, Josef Ingenerf
Clinical care and research data are widely dispersed in isolated systems based on heterogeneous data models. Biomedicine predominantly makes use of connected datasets based on the Semantic Web paradigm. Initiatives like Bio2RDF created Resource Description Framework (RDF) versions of Omics resources, enabling sophisticated Linked Data applications. In contrast, electronic healthcare records (EHR) data are generated and processed in diverse clinical subsystems within hospital information systems (HIS). Usually, each of them utilizes a relational database system with a different proprietary schema...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28421178/applying-precision-public-health-to-prevent-preterm-birth
#4
REVIEW
John P Newnham, Matthew W Kemp, Scott W White, Catherine A Arrese, Roger J Hart, Jeffrey A Keelan
Preterm birth (PTB) is one of the major health-care challenges of our time. Being born too early is associated with major risks to the child with potential for serious consequences in terms of life-long disability and health-care costs. Discovering how to prevent PTB needs to be one of our greatest priorities. Recent advances have provided hope that a percentage of cases known to be related to risk factors may be amenable to prevention; but the majority of cases remain of unknown cause, and there is little chance of prevention...
2017: Frontiers in Public Health
https://www.readbyqxmd.com/read/28418852/structural-homologies-between-phenformin-lipitor-and-gleevec-aim-the-same-metabolic-oncotarget-in-leukemia-and-melanoma
#5
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/28417609/action-plans-and-coping-strategies-in-elderly-copd-patients-influence-the-result-of-pulmonary-rehabilitation-an-observational-study
#6
Patrizia Russo, Giulia Prinzi, Aliaksei Kisialou, Vittorio Cardaci, Emanuele Stirpe, Vittoria Conti, Massimo Fini, Stefano Bonassi
BACKGROUND: COPD management needs a comprehensive assessment of clinical features (symptoms severity, co-morbidities) together with life-style, behavioural, socio-economic and multi-omics parameters. Among the other issues, psycho-cognitive assessment plays a critical role. Coping strategies are used to manage psychological stress. AIM: To evaluate the association between coping strategies and outcome of Pulmonary Rehabilitation (PR). DESIGN: Observational study...
April 14, 2017: European Journal of Physical and Rehabilitation Medicine
https://www.readbyqxmd.com/read/28417080/applying-a-systems-approach-to-thyroid-physiology-looking-at-the-whole-with-a-mitochondrial-perspective-instead-of-judging-single-tsh-values-or-why-we-should-know-more-about-mitochondria-to-understand-metabolism
#7
REVIEW
Roy Moncayo, Helga Moncayo
Classical thinking in endocrine physiology squeezes our diagnostic handling into a simple negative feedback mechanism with a controller and a controlled variable. In the case of the thyroid this is reduced to TSH and fT3 and fT4, respectively. The setting of this tight notion has no free space for any additions. In this paper we want to challenge this model of limited application by proposing a construct based on a systems approach departing from two basic considerations. In first place since the majority of cases of thyroid disease develop and appear during life it has to be considered as an acquired condition...
June 2017: BBA Clinical
https://www.readbyqxmd.com/read/28415856/gene-and-variant-annotation-for-mendelian-disorders-in-the-era-of-advanced-sequencing-technologies
#8
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/28414282/-pharmacometabonomics-the-novel-way-to-personalized-drug-therapy
#9
REVIEW
D L Maslov, E E Balashova, P G Lokhov, A I Archakov
The review is devoted to pharmacometabonomics - a new branch of science focused on personalization of drug therapy through the comprehensive analysis of metabolites of patient's biological fluids. It considers the history of pharmacometabonomic, positioning to other "-omic" sciences, and system approach, realized by this science, in determination of individual therapeutic dose of the drugs and also a technical implementation of pharmacometabonomic based on direct mass spectrometry of blood plasma metabolites...
March 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/28402209/culturomics-a-new-kid-on-the-block-of-omics-to-enable-personalized-medicine
#10
Manousos E Kambouris, Cristiana Pavlidis, Efthymios Skoufas, Michael Arabatzis, Maria Kantzanou, Aristea Velegraki, George P Patrinos
This innovation analysis highlights the underestimated and versatile potential of the new field of culturomics and examines its relation to other OMICS system sciences such as infectiomics, metabolomics, phenomics, and pharmacomicrobiomics. The advent of molecular biology, followed by the emergence of various disciplines of the genomics, and most importantly metagenomics, brought about the sharp decline of conventional microbiology methods. Emergence of culturomics has a natural synergy with therapeutic and clinical genomic approaches so as to realize personalized medicine...
April 12, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28401970/integrating-multiple-omics-data-for-the-discovery-of-potential-beclin-1-interactions-in-breast-cancer
#11
Yi Chen, Xuan Wang, Guan Wang, Zhaozhi Li, Jinjin Wang, Lingyu Huang, Ziyi Qin, Xiang Yuan, Zhong Cheng, Shu Zhang, Yiqiong Yin, Jun He
Breast cancer has been reported as one of the most frequently diagnosed malignant diseases and the leading cause of cancer death in women all around the world. Furthermore, this complicated cancer is divided into multiple subtypes which present different clinical symptoms and need correspondingly directed therapy. We took BECN1, a core gene in autophagy performing a tumor inhibitory effect, as a starting point. The study in this paper aims to identify genes related to breast cancer and its multiple subtypes by integrating multiple omics data using the least absolute shrinkage and selection operator (LASSO), which is a statistical method that can integrate more than two types of omics data...
April 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28401306/toolbox-in-a-tadpole-xenopus-for-kidney-research
#12
REVIEW
Maike Getwan, Soeren S Lienkamp
Xenopus is a versatile model organism increasingly used to study organogenesis and genetic diseases. The rapid embryonic development, targeted injections, loss- and gain-of-function experiments and an increasing supply of tools for functional in vivo analysis are unique advantages of the Xenopus system. Here, we review the vast array of methods available that have facilitated its transition into a translational model. We will focus primarily on how these methods have been employed in the study of kidney development, renal function and kidney disease...
April 11, 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28391973/the-current-status-and-problems-confronted-in-delivering-precision-medicine-in-japan-and-europe
#13
REVIEW
Hideaki Bando
Precision medicine has been defined as "a predictive, preventive, personalized, and participatory health care service delivery model." Today, developments in next-generation sequencing and information technology have made precision medicine possible, with massive amounts of genetic, "omics," clinical, environmental, and lifestyle data now available. Unfortunately, differences in governmental support and health care regulations have resulted in heterogeneous progress among countries. In Japan, for example, precision cancer screening and treatments are increasingly being promoted, with collaboration among research, governmental, and pharmaceutical agencies taking place in the nationwide SCRUM-Japan cancer genome screening project...
February 22, 2017: Current Problems in Cancer
https://www.readbyqxmd.com/read/28388542/emerging-proteomics-biomarkers-and-prostate-cancer-burden-in-africa
#14
REVIEW
Henry A Adeola, Jonathan M Blackburn, Timothy R Rebbeck, Luiz F Zerbini
Various biomarkers have emerged via high throughput omics-based approaches for use in diagnosis, treatment, and monitoring of prostate cancer. Many of these have yet to be demonstrated as having value in routine clinical practice. Moreover, there is a dearth of information on validation of these emerging prostate biomarkers within African cohorts, despite the huge burden and aggressiveness of prostate cancer in men of African descent. This review focusses of the global landmark achievements in prostate cancer proteomics biomarker discovery and the potential for clinical implementation of these biomarkers in Africa...
March 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28387961/chemical-profiling-combined-with-omics-technologies-cp-omics-a-strategy-to-understand-the-compatibility-mechanisms-and-simplify-herb-formulas-in-traditional-chinese-medicines
#15
Tengfei Xu, Zifeng Pi, Shu Liu, Fengrui Song, Zhiqiang Liu
INTRODUCTION: The compatibility mechanisms of formulas in traditional Chinese medicine (TCM) are indistinct. In order to better understand the compatibility mechanisms and the quality control of the formulas, it is necessary to simplify formulas in TCM research. OBJECTIVE: Developing a novel method by multi-analysing the contents of different compounds in formula and inferred simplified formula simultaneously. METHODOLOGY: Chemical profiling combined with "omics" technologies (CP-omics) was employed in the present study...
April 7, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28386558/mathematical-and-computational-modeling-in-complex-biological-systems
#16
REVIEW
Zhiwei Ji, Ke Yan, Wenyang Li, Haigen Hu, Xiaoliang Zhu
The biological process and molecular functions involved in the cancer progression remain difficult to understand for biologists and clinical doctors. Recent developments in high-throughput technologies urge the systems biology to achieve more precise models for complex diseases. Computational and mathematical models are gradually being used to help us understand the omics data produced by high-throughput experimental techniques. The use of computational models in systems biology allows us to explore the pathogenesis of complex diseases, improve our understanding of the latent molecular mechanisms, and promote treatment strategy optimization and new drug discovery...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28376570/cancer-and-the-omics-revolution
#17
Richard J Epstein, Frank P Lin
BACKGROUND: Internal medicine is in flux because of the 'omics revolution', with cancer medicine being a good example. Molecular technologies that detect alterations in gene-based structure or function are having an impact on diagnosis, prognosis and treatment of cancer. OBJECTIVE: In this article, recent advances in gene-based characterisation of cancer are presented, and illustrated where possible by clinical applications. DISCUSSION: The research-based vision of precision medicine is now on its way to becoming a clinical reality...
2017: Australian Family Physician
https://www.readbyqxmd.com/read/28373857/alzheimer-s-disease-biomarkers-in-the-genome-blood-and-cerebrospinal-fluid
#18
REVIEW
Rose Ann Huynh, Chandra Mohan
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that slowly destroys memory and thinking skills, resulting in behavioral changes. It is estimated that nearly 36 million are affected globally with numbers reaching 115 million by 2050. AD can only be definitively diagnosed at autopsy since its manifestations of senile plaques and neurofibrillary tangles throughout the brain cannot yet be fully captured with current imaging technologies. Current AD therapeutics have also been suboptimal. Besides identifying markers that distinguish AD from controls, there has been a recent drive to identify better biomarkers that can predict the rates of cognitive decline and neocortical amyloid burden in those who exhibit preclinical, prodromal, or clinical AD...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28373484/moving-beyond-bermuda-sharing-data-to-build-a-medical-information-commons
#19
Robert Cook-Deegan, Amy L McGuire
The ubiquity of DNA sequencing and the advent of medical imaging, electronic health records and "omics" technologies have produced a deluge of data. Making meaning of those data - creating scientific knowledge and useful clinical information - will vastly exceed the capacity of even the largest institutions. Data must be shared to achieve the promise of genomic science and precision medicine.
April 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28373404/precancer-atlas-to-drive-precision-prevention-trials
#20
Avrum Spira, Matthew B Yurgelun, Ludmil Alexandrov, Anjana Rao, Rafael Bejar, Kornelia Polyak, Marios Giannakis, Ali Shilatifard, Olivera J Finn, Madhav Dhodapkar, Neil E Kay, Esteban Braggio, Eduardo Vilar, Sarah A Mazzilli, Timothy R Rebbeck, Judy E Garber, Victor E Velculescu, Mary L Disis, Douglas C Wallace, Scott M Lippman
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape...
April 1, 2017: Cancer Research
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