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https://www.readbyqxmd.com/read/28935855/establishing-multiple-omics-baselines-for-three-southeast-asian-populations-in-the-singapore-integrative-omics-study
#1
Woei-Yuh Saw, Erwin Tantoso, Husna Begum, Lihan Zhou, Ruiyang Zou, Cheng He, Sze Ling Chan, Linda Wei-Lin Tan, Lai-Ping Wong, Wenting Xu, Don Kyin Nwe Moong, Yenly Lim, Bowen Li, Nisha Esakimuthu Pillai, Trevor A Peterson, Tomasz Bielawny, Peter J Meikle, Piyushkumar A Mundra, Wei-Yen Lim, Ma Luo, Kee-Seng Chia, Rick Twee-Hee Ong, Liam R Brunham, Chiea-Chuen Khor, Heng Phon Too, Richie Soong, Markus R Wenk, Peter Little, Yik-Ying Teo
The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups...
September 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28933618/novel-cns-drug-discovery-and-development-approach-model-based-integration-to-predict-neuro-pharmacokinetics-and-pharmacodynamics
#2
Elizabeth C M de Lange, Willem van den Brink, Yumi Yamamoto, Wilhelmus E A de Witte, Yin Cheong Wong
CNS drug development has been hampered by inadequate consideration of CNS pharmacokinetic (PK), pharmacodynamics (PD) and disease complexity (reductionist approach). Improvement is required via integrative model-based approaches. Areas covered: The authors summarize factors that have played a role in the high attrition rate of CNS compounds. Recent advances in CNS research and drug discovery are presented, especially with regard to assessment of relevant neuro-PK parameters. Suggestions for further improvements are also discussed...
September 21, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28933291/pharmacotranscriptomic-biomarkers-in-glucocorticoid-treatment-of-pediatric-inflammatory-bowel-disease
#3
Marianna Lucafò, Biljana Stankovic, Nikola Kotur, Alessia Di Silvestre, Stefano Martelossi, Alessandro Ventura, Branka Zukic, Sonya Pavlovic, Giuliana Decorti
Pharmacotranscriptomics aims to reach more accurate drug dosing based on interindividual transcriptome variations. Here, we provide an overview of RNA biomarkers that could predict the response to glucocorticoids (GCs), considered the standard for treatment of inflammatory bowel diseases (IBD), both in adult and pediatric patients. Although new biological agents are very effective in the IBD treatment, GCs are still widely used for induction of remission in IBD patients with moderate to severe disease. It is important to identify patients that are poor responders to GCs therapy, because suboptimal response is frequent and associated with various side effects...
September 20, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28929814/what-s-new-in-the-diagnosis-of-pancreatic-cancer-a-patent-review-2011-present
#4
Houria Boulaiz, María C Ramos, Carmen Griñán-Lisón, Maria E García-Rubiño, Francisca Vicente, Juan Antonio Marchal
Pancreatic cancer (PC) is the fourth leading cause of cancer-related death in the US with a 5-year survival rate of about 5%. Most patients have advanced metastatic disease mainly due to the lack of an effective early detection, and an extremely poor prognosis. Advancing in the fight against PC requires developing novel observable biomarkers at preclinical stages for early detection. Areas covered: This manuscript is an overview of different PC diagnostic modalities and the latest innovations made to enhance early PC detection through the patents published from 2011 to 2017...
September 20, 2017: Expert Opinion on Therapeutic Patents
https://www.readbyqxmd.com/read/28929311/tbi-rehabilomics-research-an-exemplar-of-a-biomarker-based-approach-to-precision-care-for-populations-with-disability
#5
REVIEW
Amy K Wagner
PURPOSE OF REVIEW: The purpose of this review is to summarize how "-omics" technologies can inform rehabilitation-relevant outcomes for a range of populations with neurologically related disability by including outcome metrics linked to the World Health Organization's International Classification of Functioning, Disability, and Health (WHO-ICF) domains of impairments in body function, activity limitations, and participation restrictions. RECENT FINDINGS: To date, nearly every area of medicine uses biomarkers in some capacity to aid in understanding how personal biology informs clinical care...
September 19, 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28926971/mini-review-the-contribution-of-intermediate-phenotypes-to-gxe-effects-on-disorders-of-body-composition-in-the-new-omics-era
#6
REVIEW
Edna J Nava-Gonzalez, Esther C Gallegos-Cabriales, Irene Leal-Berumen, Raul A Bastarrachea
Studies of gene-environment (GxE) interactions describe how genetic and environmental factors influence the risk of developing disease. Intermediate (molecular or clinical) phenotypes (IPs) are traits or metabolic biomarkers that mediate the effects of gene-environment influences on risk behaviors. Functional systems genomics discovery offers mechanistic insights into how DNA variations affect IPs in order to detect genetic causality for a given disease. Disorders of body composition include obesity (OB), Type 2 diabetes (T2D), and osteoporosis (OSTP)...
September 17, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28923369/rapid-identification-and-validation-of-novel-targeted-approaches-for-glioblastoma-a-combined-ex-vivo-in-vivo-pharmaco-omic-model
#7
REVIEW
Ahmad Daher, John de Groot
Tumor heterogeneity is a major factor in glioblastoma's poor response to therapy and seemingly inevitable recurrence. Only two glioblastoma drugs have received Food and Drug Administration approval since 1998, highlighting the urgent need for new therapies. Profiling "omics" analyses have helped characterize glioblastoma molecularly and have thus identified multiple molecular targets for precision medicine. These molecular targets have influenced clinical trial design; many "actionable" mutation-focused trials are underway, but because they have not yet led to therapeutic breakthroughs, new strategies for treating glioblastoma, especially those with a pharmacological functional component, remain in high demand...
September 15, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28917669/knowledge-driven-computational-modeling-in-alzheimer-s-research-current-state-and-future-trends
#8
Hugo Geerts, Martin Hofmann-Apitius, Thomas J Anastasio
Neurodegenerative diseases such as Alzheimer's disease (AD) follow a slowly progressing dysfunctional trajectory, with a large presymptomatic component and many comorbidities. Using preclinical models and large-scale omics studies ranging from genetics to imaging, a large number of processes that might be involved in AD pathology at different stages and levels have been identified. The sheer number of putative hypotheses makes it almost impossible to estimate their contribution to the clinical outcome and to develop a comprehensive view on the pathological processes driving the clinical phenotype...
September 14, 2017: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
https://www.readbyqxmd.com/read/28917272/towards-personalized-medicine-of-colorectal-cancer
#9
REVIEW
Mohammad Azhar Aziz, Zeyad Yousef, Ayman M Saleh, Sameer Mohammad, Bandar Al Knawy
Efforts in colorectal cancer (CRC) research aim to improve early detection and treatment for metastatic stages which could translate into better prognosis of this disease. One of the major challenges that hinder these efforts is the heterogeneous nature of CRC and involvement of diverse molecular pathways. New large-scale 'omics' technologies are making it possible to generate, analyze and interpret biological data from molecular determinants of CRC. The developments of sophisticated computational analyses would allow information from different omics platforms to be integrated, thus providing new insights into the biology of CRC...
October 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/28916927/genetic-test-risk-prediction-and-counseling
#10
Maggie Haitian Wang, Haoyi Weng
Advancement in technology has nurtured the new era of genetic tests for personalized medicine. In this chapter, we will introduce the current development, challenges, and the outlook of genetic test, disease risk prediction, and genetic counseling. In the first section, we will present the success cases in the areas of molecular classification of tumors, pharmacogenomics, and Mendelian disorders, and the challenges of genetic tests implementations. In the second section, common methods for genetic risk prediction models and evaluation measures will be introduced, as well as challenges in feature reliability, risk model stability, and clinical utility...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28913985/asthma-biomarkers-do-they-bring-precision-medicine-closer-to-the-clinic
#11
REVIEW
Ioana Agache, Liliana Rogozea
Measurement of biomarkers has been incorporated within clinical research of asthma to characterize the population and to associate the disease with environmental and therapeutic effects. Regrettably, at present, there are no specific biomarkers, none is validated or qualified, and endotype-driven choices overlap. Biomarkers have not yet reached clinical practice and are not included in current asthma guidelines. Last but not least, the choice of the outcome upholding the value of the biomarkers is extremely difficult, since it has to reflect the mechanistic intervention while being relevant to both the disease and the particular person...
November 2017: Allergy, Asthma & Immunology Research
https://www.readbyqxmd.com/read/28900867/recent-advances-in-the-etiopathogenesis-of-inflammatory-bowel-disease-the-role-of-omics
#12
REVIEW
Eleni Stylianou
Omics technology presents an exciting and timely opportunity to improve our understanding of the molecular etiology and pathogenesis of the group of chronic, heterogeneous, inflammatory disorders that comprise inflammatory bowel disease (IBD). Interest in the use of omics in the biomedical and clinical research communities is gaining pace due to its potential to make huge strides in our understanding of IBD causality, and pathology. Omics-related research also has applicability for biomarker discovery and the development of individualized treatments for patients, termed 'precision medicine'...
September 12, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28898880/personalized-management-of-cardiovascular-disorders
#13
Kewal K Jain
Personalized management of cardiovascular disorders (CVDs), also referred to as personalized or precision cardiology in accordance with general principles of personalized medicine, is the selection of best treatment for an individual patient. It involves the integration of various 'omics' technologies such as genomics and proteomics as well as other new technologies such as nanobiotechnology. Molecular diagnostics and biomarkers are important for linking diagnosis with therapy and monitoring of therapy. Because CVDs involve perturbations of large complex biological networks, a systems biology approach to CVD risk stratification may be used for improving risk-estimating algorithms and modeling of personalized benefit-of-treatment may be helpful for guiding choice of intervention...
September 11, 2017: Medical Principles and Practice: International Journal of the Kuwait University, Health Science Centre
https://www.readbyqxmd.com/read/28887085/visualizing-omics-and-clinical-data-which-challenges-for-dealing-with-their-variety
#14
REVIEW
Fleur Mougin, David Auber, Romain Bourqui, Gayo Diallo, Isabelle Dutour, Vianney Jouhet, Frantz Thiessard, Rodolphe Thiébaut, Patricia Thébault
Life sciences are currently going through a great number of transformations raised by the in-going revolution in high-throughput technologies for the acquisition of data. The integration of their high dimensionality, ranging from omics to clinical data, is becoming one of the most challenging stages. It involves inter-disciplinary developments with the aim to move towards an enhanced understanding of human physiology for caring purposes. Biologists, bioinformaticians, physicians and other experts related to the healthcare domain have to accompany each step of the analysis process in order to investigate and expertise these various data...
September 6, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28878238/apobec3a-is-an-oral-cancer-prognostic-biomarker-in-taiwanese-carriers-of-an-apobec-deletion-polymorphism
#15
Ting-Wen Chen, Chi-Ching Lee, Hsuan Liu, Chi-Sheng Wu, Curtis R Pickering, Po-Jung Huang, Jing Wang, Ian Yi-Feng Chang, Yuan-Ming Yeh, Chih-De Chen, Hsin-Pai Li, Ji-Dung Luo, Bertrand Chin-Ming Tan, Timothy En Haw Chan, Chuen Hsueh, Lichieh Julie Chu, Yi-Ting Chen, Bing Zhang, Chia-Yu Yang, Chih-Ching Wu, Chia-Wei Hsu, Lai-Chu See, Petrus Tang, Jau-Song Yu, Wei-Chao Liao, Wei-Fan Chiang, Henry Rodriguez, Jeffrey N Myers, Kai-Ping Chang, Yu-Sun Chang
Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n = 188; p = 0...
September 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28874669/phenotype-driven-precision-oncology-as-a-guide-for-clinical-decisions-one-patient-at-a-time
#16
Shumei Chia, Joo-Leng Low, Xiaoqian Zhang, Xue-Lin Kwang, Fui-Teen Chong, Ankur Sharma, Denis Bertrand, Shen Yon Toh, Hui-Sun Leong, Matan T Thangavelu, Jacqueline S G Hwang, Kok-Hing Lim, Thakshayeni Skanthakumar, Hiang-Khoon Tan, Yan Su, Siang Hui Choo, Hannes Hentze, Iain B H Tan, Alexander Lezhava, Patrick Tan, Daniel S W Tan, Giridharan Periyasamy, Judice L Y Koh, N Gopalakrishna Iyer, Ramanuj DasGupta
Genomics-driven cancer therapeutics has gained prominence in personalized cancer treatment. However, its utility in indications lacking biomarker-driven treatment strategies remains limited. Here we present a "phenotype-driven precision-oncology" approach, based on the notion that biological response to perturbations, chemical or genetic, in ex vivo patient-individualized models can serve as predictive biomarkers for therapeutic response in the clinic. We generated a library of "screenable" patient-derived primary cultures (PDCs) for head and neck squamous cell carcinomas that reproducibly predicted treatment response in matched patient-derived-xenograft models...
September 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28873014/impact-of-preanalytical-variations-in-blood-derived-biospecimens-on-omics-studies-toward-precision-biobanking
#17
Jae-Eun Lee, Young-Youl Kim
Research data and outcomes do vary across populations and persons, but this is not always due to experimental or true biological variation. Preanalytical components of experiments, be they biospecimen acquisition, preparation, storage, or transportation to the laboratory, may all contribute to apparent variability in research data, outcomes, and interpretation. The present review article and biobanking innovation analysis offer new insights with a summary of such preanalytical variables, for example, the type of blood collection tube, centrifugation conditions, long-term sample storage temperature, and duration, on output of omics analyses of blood-derived biospecimens: whole blood, serum, plasma, buffy coat, and peripheral blood mononuclear cells...
September 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28871446/mechanisms-and-clinical-implications-of-tumor-heterogeneity-and-convergence-on-recurrent-phenotypes
#18
REVIEW
Jasmine A McQuerry, Jeffrey T Chang, David D L Bowtell, Adam Cohen, Andrea H Bild
Tumor heterogeneity has been identified at various -omic levels. The tumor genome, transcriptome, proteome, and phenome can vary widely across cells in patient tumors and are influenced by tumor cell interactions with heterogeneous physical conditions and cellular components of the tumor microenvironment. Here, we explore the concept that while variation exists at multiple -omic levels, changes at each of these levels converge on the same pathways and lead to convergent phenotypes in tumors that can provide common drug targets...
September 4, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28869846/a-statistical-framework-for-applying-rna-profiling-to-chemical-hazard-detection
#19
REVIEW
Mitchell S Kostich
Use of 'omics technologies in environmental science is expanding. However, application is mostly restricted to characterizing molecular steps leading from toxicant interaction with molecular receptors to apical endpoints in laboratory species. Use in environmental decision-making is limited, due to difficulty in elucidating mechanisms in sufficient detail to make quantitative outcome predictions in any single species or in extending predictions to aquatic communities. Here we introduce a mechanism-agnostic statistical approach, supplementing mechanistic investigation by allowing probabilistic outcome prediction even when understanding of molecular pathways is limited, and facilitating extrapolation from results in laboratory test species to predictions about aquatic communities...
August 28, 2017: Chemosphere
https://www.readbyqxmd.com/read/28868294/integration-of-proteomics-and-metabolomics-in-exploring-genetic-and-rare-metabolic-diseases
#20
REVIEW
Michele Costanzo, Miriam Zacchia, Giuliana Bruno, Daniela Crisci, Marianna Caterino, Margherita Ruoppolo
BACKGROUND: Inherited metabolic disorders or inborn errors of metabolism are caused by deficiency of enzymatic activities in the catabolism of amino acids, carbohydrates, or lipids. These disorders include aminoacidopathies, urea cycle defects, organic acidemias, defects of oxidation of fatty acids, and lysosomal storage diseases. Inborn errors of metabolism constitute a significant proportion of genetic diseases, particularly in children; however, they are individually rare. Clinical phenotypes are very variable, some of them remain asymptomatic, others manifest metabolic decompensation in neonatal age, and others encompass mental retardation at later age...
July 2017: Kidney Diseases
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