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Clinical omics

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https://www.readbyqxmd.com/read/28643821/non-invasive-approaches-in-the-diagnosis-of-acute-rejection-in-kidney-transplant-recipients-part-i-in-vivo-imaging-methods
#1
REVIEW
Oriane Hanssen, Pauline Erpicum, Pierre Lovinfosse, Paul Meunier, Laurent Weekers, Luaba Tshibanda, Jean-Marie Krzesinski, Roland Hustinx, François Jouret
Kidney transplantation (KTx) represents the best available treatment for patients with end-stage renal disease. Still, full benefits of KTx are undermined by acute rejection (AR). The diagnosis of AR ultimately relies on transplant needle biopsy. However, such an invasive procedure is associated with a significant risk of complications and is limited by sampling error and interobserver variability. In the present review, we summarize the current literature about non-invasive approaches for the diagnosis of AR in kidney transplant recipients (KTRs), including in vivo imaging, gene expression profiling and omics analyses of blood and urine samples...
February 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28643819/non-invasive-approaches-in-the-diagnosis-of-acute-rejection-in-kidney-transplant-recipients-part-ii-omics-analyses-of-urine-and-blood-samples
#2
REVIEW
Pauline Erpicum, Oriane Hanssen, Laurent Weekers, Pierre Lovinfosse, Paul Meunier, Luaba Tshibanda, Jean-Marie Krzesinski, Roland Hustinx, François Jouret
Kidney transplantation (KTx) represents the best available treatment for patients with end-stage renal disease. Still, the full benefits of KTx are undermined by acute rejection (AR). The diagnosis of AR ultimately relies on transplant needle biopsy. However, such an invasive procedure is associated with a significant risk of complications and is limited by sampling error and interobserver variability. In the present review, we summarize the current literature about non-invasive approaches for the diagnosis of AR in kidney transplant recipients (KTRs), including in vivo imaging, gene-expression profiling and omics analyses of blood and urine samples...
February 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28638489/harnessing-integrative-omics-to-facilitate-molecular-imaging-of-the-human-epidermal-growth-factor-receptor-family-for-precision-medicine
#3
REVIEW
Martin Pool, H Rudolf de Boer, Marjolijn N Lub-de Hooge, Marcel A T M van Vugt, Elisabeth G E de Vries
Cancer is a growing problem worldwide. The cause of death in cancer patients is often due to treatment-resistant metastatic disease. Many molecularly targeted anticancer drugs have been developed against 'oncogenic driver' pathways. However, these treatments are usually only effective in properly selected patients. Resistance to molecularly targeted drugs through selective pressure on acquired mutations or molecular rewiring can hinder their effectiveness. This review summarizes how molecular imaging techniques can potentially facilitate the optimal implementation of targeted agents...
2017: Theranostics
https://www.readbyqxmd.com/read/28638442/computational-dynamic-approaches-for-temporal-omics-data-with-applications-to-systems-medicine
#4
REVIEW
Yulan Liang, Arpad Kelemen
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for understanding the complexity of the human health, drug response, disease susceptibility and pathogenesis for systems medicine. Temporal omics data used to measure the dynamic biological systems are essentials to discover complex biological interactions and clinical mechanism and causations. However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for which conventional experimental techniques are not suited in the big omics era...
2017: BioData Mining
https://www.readbyqxmd.com/read/28627406/multi-omics-facilitated-variable-selection-in-cox-regression-model-for-cancer-prognosis-prediction
#5
Cong Liu, Xujun Wang, Georgi Z Genchev, Hui Lu
Motivation New developments in high-throughput genomic technologies have enabled the measurement of diverse types of omics biomarkers in a cost-efficient and clinically-feasible manner. Developing computational methods and tools for analysis and translation of such genomic data into clinically-relevant information is an ongoing and active area of investigation. For example, several studies have utilized an unsupervised learning framework to cluster patients by integrating omics data. Despite such recent advances, predicting cancer prognosis using integrated omics biomarkers remains a challenge...
June 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28624903/early-diagnosis-of-sepsis-is-an-integrated-omics-approach-the-way-forward
#6
REVIEW
Raymond J Langley, Hector R Wong
Sepsis remains one of the leading causes of death in the USA and it is expected to get worse as the population ages. Moreover, the standard of care, which recommends aggressive treatment with appropriate antibiotics, has led to an increase in multiple drug-resistant organisms. There is a dire need for the development of new antibiotics, improved antibiotic stewardship, and therapies that treat the host response. Development of new sepsis therapeutics has been a disappointment as no drugs are currently approved to treat the various complications from sepsis...
June 17, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28618973/from-clinical-uncertainties-to-precision-medicine-the-emerging-role-of-the-gut-barrier-and-microbiome-in-small-bowel-functional-diseases
#7
Wojciech Marlicz, Diana Yung, Karolina Skonieczna-Żydecka, Igor Loniewski, Saskia van Hemert, Beata Loniewska, Anastasios Koulaouzidis
Over the last decade, remarkable progress has been made in the understanding of disease pathophysiology. Many new theories expound on the importance of emerging factors such as microbiome influences, genomics/omics, stem cells, innate intestinal immunity or mucosal barrier complexities. This has introduced a further dimension of uncertainty into clinical decision-making, but equally, may shed some light on less well-understood and difficult to manage conditions. Areas covered: Comprehensive review of the literature on gut barrier and microbiome relevant to small bowel pathology...
June 16, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28618240/omics-for-precious-rare-biosamples-characterization-of-ancient-human-hair-by-a-proteomic-approach
#8
Margaux Fresnais, Pascale Richardin, Marcela Sepúlveda, Emmanuelle Leize-Wagner, Armelle Charrié-Duhaut
Omics technologies have far-reaching applications beyond clinical medicine. A case in point is the analysis of ancient hair samples. Indeed, hair is an important biological indicator that has become a material of choice in archeometry to study the ancient civilizations and their environment. Current characterization of ancient hair is based on elemental and structural analyses, but only few studies have focused on the molecular aspects of ancient hair proteins-keratins-and their conservation state. In such cases, applied extraction protocols require large amounts of raw hair, from 30 to 100 mg...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28618012/metabolomic-signature-of-brain-cancer
#9
Renu Pandey, Laura Caflisch, Alessia Lodi, Andrew J Brenner, Stefano Tiziani
Despite advances in surgery and adjuvant therapy, brain tumours represent one of the leading causes of cancer-related mortality and morbidity in both adults and children. Gliomas constitute about 60% of all cerebral tumours, showing varying degrees of malignancy. They are difficult to treat due to dismal prognosis and limited therapeutics. Metabolomics is the untargeted and targeted analyses of endogenous and exogenous small molecules, which characterizes the phenotype of an individual. This emerging "omics" science provides functional readouts of cellular activity that contribute greatly to the understanding of cancer biology including brain tumour biology...
June 15, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28615163/understanding-mechanisms-and-seeking-cures-for-alzheimer-s-disease-why-we-must-be-extraordinarily-diverse
#10
Madhav Thambisetty
After more than a century since Dr. Alois Alzheimer first described the pathological hallmarks accompanying the defining clinical features of the disease, we have yet to deliver any meaningful disease-modifying treatments to our patients. In this article, we present a rationale for the need to be "extraordinarily diverse" in seeking effective ways to treat or prevent this devastating disease. Our approach is based on applying a systems-biology perspective at the population level, using a diverse array of 'OMICS' methodologies to identify molecular mechanisms associated with well-established AD risk factors including systemic inflammation, obesity and insulin resistance...
June 14, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/28613106/innovative-array-based-assay-for-omics-pattern-in-melanoma
#11
Carmen Dumitru, Carolina Constantin, Cristiana Popp, Mirela Cioplea, Sabina Zurac, Tatiana Vassu, Monica Neagu
Cutaneous melanoma remains a major health issue and still an important challenge for research. Thus omics complex evaluation can provide a more specific molecular classification for this heterogeneous disease. Complex omics analysis based on genomic and proteomic microarrays can identify disease markers that prognosticate disease evolution or can monitor therapies efficacy. Among the technologies that gained momentum in the last years, array based comparative genomic hybridization offered the possibility to analyze chromosomal numerical aberrations within cutaneous melanomas providing important support for molecular classification of melanoma tumors...
June 14, 2017: Journal of Immunoassay & Immunochemistry
https://www.readbyqxmd.com/read/28611656/dissecting-the-molecular-mechanisms-of-neurodegenerative-diseases-through-network-biology
#12
Jose A Santiago, Virginie Bottero, Judith A Potashkin
Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/28604114/an-omics-perspective-to-the-molecular-mechanisms-of-anticancer-metallo-drugs-in-the-computational-microscope-era
#13
Angelo Spinello, Alessandra Magistrato
Metallo-drugs have attracted enormous interest for cancer treatment. The achievements of this drug-type are summarized by the success story of cisplatin. That being said, there have been many drawbacks with its clinical use, which prompted decades worth of research efforts to move towards safer and more effective agents, either containing platinum or different metals. Areas covered: In this review, the authors provide an atomistic picture of the molecular mechanisms involving selected metallo-drugs from structural and molecular simulation studies...
June 21, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28601027/a-semantic-interoperability-approach-to-support-integration-of-gene-expression-and-clinical-data-in-breast-cancer
#14
Raul Alonso-Calvo, Sergio Paraiso-Medina, David Perez-Rey, Enrique Alonso-Oset, Ruud van Stiphout, Sheng Yu, Marian Taylor, Francesca Buffa, Carlos Fernandez-Lozano, Alejandro Pazos, Victor Maojo
INTRODUCTION: The introduction of omics data and advances in technologies involved in clinical treatment has led to a broad range of approaches to represent clinical information. Within this context, patient stratification across health institutions due to omic profiling presents a complex scenario to carry out multi-center clinical trials. METHODS: This paper presents a standards-based approach to ensure semantic integration required to facilitate the analysis of clinico-genomic clinical trials...
June 5, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28597939/precision-oncology-based-on-omics-data-the-nct-heidelberg-experience
#15
Peter Horak, Barbara Klink, Christoph Heining, Stefan Gröschel, Barbara Hutter, Martina Fröhlich, Sebastian Uhrig, Daniel Hübschmann, Matthias Schlesner, Roland Eils, Daniela Richter, Katrin Pfütze, Christina Geörg, Bettina Meißburger, Stephan Wolf, Angela Schulz, Roland Penzel, Esther Herpel, Martina Kirchner, Amelie Lier, Volker Endris, Stephan Singer, Peter Schirmacher, Wilko Weichert, Albrecht Stenzinger, Richard F Schlenk, Evelin Schröck, Benedikt Brors, Christof von Kalle, Hanno Glimm, Stefan Fröhling
Precision oncology implies the ability to predict which patients will likely respond to specific cancer therapies based on increasingly accurate, high-resolution molecular diagnostics as well as the functional and mechanistic understanding of individual tumors. While molecular stratification of patients can be achieved through different means, a promising approach is next-generation sequencing of tumor DNA and RNA, which can reveal genomic alterations that have immediate clinical implications. Furthermore, certain genetic alterations are shared across multiple histologic entities, raising the fundamental question of whether tumors should be treated by molecular profile and not tissue of origin...
June 9, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28597766/identifying-super-responders-in-pulmonary-arterial-hypertension
#16
Stephen J Halliday, Anna R Hemnes
Pharmacotherapeutic options for pulmonary arterial hypertension (PAH) have increased dramatically in the last two decades and along with this have been substantial improvements in survival. Despite these advances, however, PAH remains a progressive and ultimately fatal disease for most patients and only epoprostenol has been shown to improve survival in a randomized control trial. Clinical observations of the heterogeneity of treatment response to different classes of medications across the phenotypically diverse PAH population has led to the identification of patients who derive significantly more benefit from certain medications than the population mean, the so-called "super responders...
April 2017: Pulmonary Circulation
https://www.readbyqxmd.com/read/28589087/nodular-thyroid-disease-and-thyroid-cancer-in-the-era-of-precision-medicine
#17
REVIEW
Carles Zafon, Juan J Díez, Juan C Galofré, David S Cooper
The management of thyroid nodules, one of the main clinical challenges in endocrine clinical practice, is usually straightforward. Although the most important concern is ruling out malignancy, there are grey areas where uncertainty is frequently present: the nodules labelled as indeterminate by cytology and the extent of therapy when thyroid cancer is diagnosed pathologically. There is evidence that the current available precision medicine tools (from all the "-omics" to molecular analysis, fine-tuning imaging or artificial intelligence) may help to fill present gaps in the future...
April 2017: European Thyroid Journal
https://www.readbyqxmd.com/read/28583306/developing-and-utilizing-controlled-human-models-of-infection
#18
Chad K Porter, A Louis Bourgeois, Robert W Frenck, Michael Prouty, Nicole Maier, Mark S Riddle
The controlled human infection model (CHIM) to assess the efficacy of vaccines against Shigella and enterotoxigenic Escherichia coli (ETEC) has several unique features that could significantly enhance the ability to test candidate vaccines. Despite increasing interest in these models, questions remain as to how to best incorporate them into vaccine development and how to maximize results. We designed a workshop focused on CHIM as part of the Vaccines Against Shigella and ETEC (VASE) Conference. The workshop, using the World Café method, focused on; clinical outcomes, nonclinical outcomes and model standardization...
June 2, 2017: Vaccine
https://www.readbyqxmd.com/read/28582486/jdinac-joint-density-based-non-parametric-differential-interaction-network-analysis-and-classification-using-high-dimensional-sparse-omics-data
#19
Jiadong Ji, Di He, Yang Feng, Yong He, Fuzhong Xue, Lei Xie
Motivation: A complex disease is usually driven by a number of genes interwoven into networks, rather than a single gene product. Network comparison or differential network analysis has become an important means of revealing the underlying mechanism of pathogenesis and identifying clinical biomarkers for disease classification. Most studies, however, are limited to network correlations that mainly capture the linear relationship among genes, or rely on the assumption of a parametric probability distribution of gene measurements...
June 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28577718/intrahepatic-cholangiocarcinoma-molecular-markers-for-diagnosis-and-prognosis
#20
REVIEW
Amir A Rahnemai-Azar, Allison Weisbrod, Mary Dillhoff, Carl Schmidt, Timothy M Pawlik
Intrahepatic cholangiocarcinoma (iCCA) is the second most common primary liver tumor with increasing incidence worldwide. The outcome of patients with iCCA is dismal owing to tumor's aggressiveness, late diagnosis and lack of effective treatment options. Detection of the tumor at early stages may make surgical resection, as only potential curative treatment, more feasible. Unfortunately, despite recent developments in imaging modalities and laboratory tests, the diagnosis of iCCA remains challenging and patients often present in advanced stages when surgery cannot be offered...
June 2017: Surgical Oncology
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