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Clinical omics

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https://www.readbyqxmd.com/read/28327601/bcip-a-gene-centered-platform-for-identifying-potential-regulatory-genes-in-breast-cancer
#1
Jiaqi Wu, Shuofeng Hu, Yaowen Chen, Zongcheng Li, Jian Zhang, Hanyu Yuan, Qiang Shi, Ningsheng Shao, Xiaomin Ying
Breast cancer is a disease with high heterogeneity. Many issues on tumorigenesis and progression are still elusive. It is critical to identify genes that play important roles in the progression of tumors, especially for tumors with poor prognosis such as basal-like breast cancer and tumors in very young women. To facilitate the identification of potential regulatory or driver genes, we present the Breast Cancer Integrative Platform (BCIP, http://omics.bmi.ac.cn/bcancer/). BCIP maintains multi-omics data selected with strict quality control and processed with uniform normalization methods, including gene expression profiles from 9,005 tumor and 376 normal tissue samples, copy number variation information from 3,035 tumor samples, microRNA-target interactions, co-expressed genes, KEGG pathways, and mammary tissue-specific gene functional networks...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28324299/fatal-familial-insomnia-clinical-aspects-and-molecular-alterations
#2
REVIEW
Franc Llorens, Juan-José Zarranz, Andre Fischer, Inga Zerr, Isidro Ferrer
PURPOSE OF REVIEW: Fatal familiar insomnia (FFI) is an autosomal dominant inherited prion disease caused by D178N mutation in the prion protein gene (PRNP D178N) accompanied by the presence of a methionine at the codon 129 polymorphic site on the mutated allele. FFI is characterized by severe sleep disorder, dysautonomia, motor signs and abnormal behaviour together with primary atrophy of selected thalamic nuclei and inferior olives, and expansion to other brain regions with disease progression...
April 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28321390/metabonomics-research-progress-on-liver-diseases
#3
REVIEW
Mengqian Yu, Ying Zhu, Qingwei Cong, Chunyan Wu
Metabolomics as the new omics technique develops after genomics, transcriptomics, and proteomics and has rapid development at present. Liver diseases are worldwide public health problems. In China, chronic hepatitis B and its secondary diseases are the common liver diseases. They can be diagnosed by the combination of history, virology, liver function, and medical imaging. However, some patients seldom have relevant physical examination, so the diagnosis may be delayed. Many other liver diseases, such as drug-induced liver injury (DILI), alcoholic liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD), and autoimmune liver diseases, still do not have definite diagnostic markers; the diagnosis consists of history, medical imaging, and the relevant score...
2017: Canadian Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28302550/the-22q11-2-deletion-syndrome-in-congenital-heart-defects-prevalence-of-microdeletion-syndrome-in-cameroon
#4
Ambroise Wonkam, Ricardo Toko, David Chelo, Cedrik Tekendo-Ngongang, Samuel Kingue, Sophie Dahoun
BACKGROUND: The 22q11.2 deletion syndrome is amongst the most common microdeletion syndrome in humans. Its prevalence remains unknown in sub-Saharan Africa, and its clinical features are under-reported for people of African descent. OBJECTIVE: We have investigated the prevalence of the 22q11.2 deletion syndrome in patients with congenital heart defects in Cameroon. METHODS: A total of 70 of 100 cases of congenital cardiac malformation with echocardiographic evidence were examined prospectively and tested for the 22q11...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28302035/translational-multimodality-neuroimaging
#5
Sushil K Sharma
Recently high-resolution, noninvasive, multimodality in-vivo molecular imaging with PET, SPECT, CT and MRI, employing fusion algorithms has revolutionized personalized medicine. However, specific radiopharmaceuticals (RPs) for the accurate diagnosis and effective treatment of progressive neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, drug addiction, and other cognitive impairments still remain in developmental phase. Currently, multimodality fusion neuroimaging is utilized for the determination of: pharmacokinetics and pre-clinical development of radiopharmaceuticals (RPs); in-vivo monitoring of stem cell transplantation therapy; nicotinic acetylcholine receptors (nAChRs) investigations; and regional cerebral blood flow and glucose metabolism in cognitively-impaired subjects employing noninvasive microPET and nano-SPECT imaging...
March 15, 2017: Current Drug Targets
https://www.readbyqxmd.com/read/28284392/diseases-of-the-synaptic-vesicle-a-potential-new-group-of-neurometabolic-disorders-affecting-neurotransmission
#6
E Cortès-Saladelafont, A Tristán-Noguero, R Artuch, X Altafaj, A Bayès, A García-Cazorla
The general concept of inborn error of metabolism is currently evolving into the interface between classical biochemistry and cellular biology. Basic neuroscience is providing increasing knowledge about the mechanisms of neurotransmission and novel related disorders are being described. There is a necessity of updating the classic concept of "inborn error of neurotransmitters (NT)" that considers mainly defects of synthesis and catabolism and transport of low weight NT molecules. Monogenic defects of the synaptic vesicle (SV), and especially those affecting the SV cycle are a potential new group of NT disorders since they end up in abnormal NT turnover and release...
November 2016: Seminars in Pediatric Neurology
https://www.readbyqxmd.com/read/28282717/path-to-personalized-medicine-for-type-2-diabetes-mellitus-reality-and-hope
#7
Hamid Reza Aghaei Meybodi, Mandana Hasanzad, Bagher Larijani
Type 2 diabetes mellitus (T2DM) is recognized as a public health problem and increasingly prevalent illness. Key elements of the guideline for diabetes care are based on evidence-based medicine approach and apply for population, not individuals. However, individualized care can improve diabetes management. Personalized medicine is otherwise called precision medicine tries to find better prediction, prevention, and intervention for T2DM individuals. Precision medicine in diabetes refers to the utility of genomics data of a patient with diabetes to provide the most effective diagnosis strategies and treatment plans...
March 2017: Acta Medica Iranica
https://www.readbyqxmd.com/read/28276747/proteogenomic-studies-on-cancer-drug-resistance-towards-biomarker-discovery-and-target-identification
#8
Shuyue Fu, Xiang Liu, Maochao Luo, Ke Xie, Edouard C Nice, Haiyuan Zhang, Canhua Huang
Chemoresistance is a major obstacle for current cancer treatment. Proteogenomics is a powerful multi-omics research field that uses customized protein sequence databases generated by genomic and transcriptomic information to identify novel genes (e.g. noncoding, mutation and fusion genes) from mass spectrometry-based proteomic data. By identifying aberrations that are differentially expressed between tumor and normal pairs, this approach can also be applied to validate protein variants in cancer, which may reveal the response to drug treatment...
March 6, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28272536/prediction-of-years-of-life-after-diagnosis-of-breast-cancer-using-omics-and-omic-by-treatment-interactions
#9
Agustín González-Reymúndez, Gustavo de Los Campos, Lucía Gutiérrez, Sophia Y Lunt, Ana I Vazquez
Breast cancer (BC) is the second most common type of cancer and a major cause of death for women. Commonly, BC patients are assigned to risk groups based on the combination of prognostic and prediction factors (eg, patient age, tumor size, tumor grade, hormone receptor status, etc). Although this approach is able to identify risk groups with different prognosis, patients are highly heterogeneous in their response to treatments. To improve the prediction of BC patients, we extended clinical models (including prognostic and prediction factors with whole-omic data) to integrate omics profiles for gene expression and copy number variants (CNVs)...
March 8, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28271979/toward-a-taxonomy-for-multi-omics-science-terminology-development-for-whole-genome-study-approaches-by-omics-technology-and-hierarchy
#10
Nina Pirih, Tanja Kunej
Omics is a form of high-throughput systems science. However, taxonomies for omics studies are limited, inviting us to rethink new ways in which we classify, prioritize, and rank various omics systems science studies. In this overarching context, the genome-wide study approaches have proliferated in number and popularity over the past decade. However, their hierarchy is not well organized and the development of attendant terminology is not controlled. In the present study, we searched the literature in PubMed and the Web of Science databases published from March 1999 to September 2016 using the keywords, including genome-wide, association, whole genome, transcriptome-wide, metabolome, epigenome, and phenome...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28266329/enhanced-understanding-of-the-host-pathogen-interaction-in-sepsis-new-opportunities-for-omic-approaches
#11
REVIEW
Cyndi Goh, Julian C Knight
Progress in sepsis research has been severely hampered by a heterogeneous disease phenotype, limiting the interpretation of clinical trials and the development of effective therapeutic interventions. Application of omics-based methodologies is advancing understanding of the dysregulated host immune response to infection in sepsis. However, the frequently elusive nature of the infecting organism in sepsis has limited efforts to understand the effect of disease heterogeneity involving the pathogen. Recent advances in nucleic acid sequencing-based pathogen analysis provide the opportunity for more accurate and comprehensive microbiological diagnosis...
March 2017: Lancet Respiratory Medicine
https://www.readbyqxmd.com/read/28263888/combined-venomics-antivenomics-and-venom-gland-transcriptome-analysis-of-the-monocoled-cobra-naja-kaouthia-from-china
#12
Ning Xu, Hong-Yan Zhao, Yin Yin, Shan-Shan Shen, Lin-Lin Shan, Chuan-Xi Chen, Yan-Xia Zhang, Jian-Fang Gao, Xiang Ji
We conducted an omics-analysis of the venom of Naja kaouthia from China. Proteomics analysis revealed six protein families [three-finger toxins (3-FTx), phospholipase A2 (PLA2), nerve growth factor, snake venom metalloproteinase (SVMP), cysteine-rich secretory protein and ohanin], and venom-gland transcriptomics analysis revealed 28 protein families from 79 unigenes. 3-FTx (56.5% in proteome/82.0% in transcriptome) and PLA2 (26.9%/13.6%) were identified as the most abundant families in venom proteome and venom-gland transcriptome...
March 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28263171/omics-markers-of-the-red-cell-storage-lesion-and-metabolic-linkage
#13
REVIEW
Angelo D'alessandro, Travis Nemkov, Julie Reisz, Monika Dzieciatkowska, Matthew J Wither, Kirk C Hansen
The introduction of omics technologies in the field of Transfusion Medicine has significantly advanced our understanding of the red cell storage lesion. While the clinical relevance of such a lesion is still a matter of debate, quantitative and redox proteomics approaches, as well quantitative metabolic flux analysis and metabolic tracing experiments promise to revolutionise our understanding of the role of blood processing strategies, inform the design and testing of novel additives or technologies (such as pathogen reduction), and evaluate the clinical relevance of donor and recipient biological variability with respect to red cell storability and transfusion outcomes...
March 2017: Blood Transfusion, Trasfusione del Sangue
https://www.readbyqxmd.com/read/28261328/label-free-data-standardization-for-clinical-metabolomics
#14
Petr G Lokhov, Dmitri L Maslov, Oleg N Kharibin, Elena E Balashova, Alexander I Archakov
BACKGROUND: In metabolomics, thousands of substances can be detected in a single assay. This capacity motivates the development of metabolomics testing, which is currently a very promising option for improving laboratory diagnostics. However, the simultaneous measurement of an enormous number of substances leads to metabolomics data often representing concentrations only in conditional units, while laboratory diagnostics generally require actual concentrations. To convert metabolomics data to actual concentrations, calibration curves need to be generated for each substance, and this process represents a significant challenge due to the number of substances that are present in the metabolomics data...
2017: BioData Mining
https://www.readbyqxmd.com/read/28253088/association-between-telomere-length-chronic-kidney-disease-and-renal-traits-a-systematic-review
#15
Oluwatoyin I Ameh, Ikechi G Okpechi, Collet Dandara, André-Pascal Kengne
Telomere length (TL) is an important biological variable that can influence a variety of disease-related complex traits as well as host-environment interactions such as drug and nutritional responses. Chronic kidney disease (CKD) is a common global health challenge especially with the currently aging world population. We conducted a PubMed database search according to the preferred reporting items for systematic reviews and meta-analysis (PRISMA) guidelines for systematic reviews. Studies in adults (18 years and above) in which TL was determined and correlated with CKD, renal traits, and function were included, while animal model studies were excluded...
March 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28252579/genome-sequencing-technologies-and-nursing-what-are-the-roles-of-nurses-and-nurse-scientists
#16
Jacquelyn Y Taylor, Michelle L Wright, Kathleen T Hickey, David E Housman
BACKGROUND: Advances in DNA sequencing technology have resulted in an abundance of personalized data with challenging clinical utility and meaning for clinicians. This wealth of data has potential to dramatically impact the quality of healthcare. Nurses are at the focal point in educating patients regarding relevant healthcare needs; therefore, an understanding of sequencing technology and utilizing these data are critical. AIM: The objective of this study was to explicate the role of nurses and nurse scientists as integral members of healthcare teams in improving understanding of DNA sequencing data and translational genomics for patients...
March 2017: Nursing Research
https://www.readbyqxmd.com/read/28249581/systems-biology-combining-human-and-animal-data-mirna-and-mrna-data-identifies-new-targets-in-ureteropelvic-junction-obstruction
#17
Theofilos Papadopoulos, Audrey Casemayou, Eric Neau, Benjamin Breuil, Cécile Caubet, Denis Calise, Barbara A Thornhill, Magdalena Bachvarova, Julie Belliere, Robert L Chevalier, Panagiotis Moulos, Dimcho Bachvarov, Benedicte Buffin-Meyer, Stéphane Decramer, Françoise Conte Auriol, Jean-Loup Bascands, Joost P Schanstra, Julie Klein
BACKGROUND: Although renal fibrosis and inflammation have shown to be involved in the pathophysiology of obstructive nephropathies, molecular mechanisms underlying evolution of these processes remain undetermined. In an attempt towards improved understanding of obstructive nephropathy and improved translatability of the results to clinical practice we have developed a systems biology approach combining omics data of both human and mouse obstructive nephropathy. RESULTS: We have studied in parallel the urinary miRNome of infants with ureteropelvic junction obstruction and the kidney tissue miRNome and transcriptome of the corresponding neonatal partial unilateral ureteral obstruction (UUO) mouse model...
March 1, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28248238/-omics-informed-drug-and-biomarker-discovery-opportunities-challenges-and-future-perspectives
#18
REVIEW
Holly Matthews, James Hanison, Niroshini Nirmalan
The pharmaceutical industry faces unsustainable program failure despite significant increases in investment. Dwindling discovery pipelines, rapidly expanding R&D budgets and increasing regulatory control, predict significant gaps in the future drug markets. The cumulative duration of discovery from concept to commercialisation is unacceptably lengthy, and adds to the deepening crisis. Existing animal models predicting clinical translations are simplistic, highly reductionist and, therefore, not fit for purpose...
September 12, 2016: Proteomes
https://www.readbyqxmd.com/read/28246019/early-diagnosis-and-prediction-of-anticancer-drug-induced-cardiotoxicity-from-cardiac-imaging-to-omics-technologies
#19
Rosalinda Madonna
Heart failure due to antineoplastic therapy remains a major cause of morbidity and mortality in oncological patients. These patients often have no prior manifestation of disease. There is therefore a need for accurate identification of individuals at risk of such events before the appearance of clinical manifestations. The present article aims to provide an overview of cardiac imaging as well as new "-omics" technologies, especially with regard to genomics and proteomics as promising tools for the early detection and prediction of cardiotoxicity and individual responses to antineoplastic drugs...
February 25, 2017: Revista Española de Cardiología
https://www.readbyqxmd.com/read/28245581/systematic-identification-and-assessment-of-therapeutic-targets-for-breast-cancer-based-on-genome-wide-rna-interference-transcriptomes
#20
Yang Liu, Xiaoyao Yin, Jing Zhong, Naiyang Guan, Zhigang Luo, Lishan Min, Xing Yao, Xiaochen Bo, Licheng Dai, Hui Bai
With accumulating public omics data, great efforts have been made to characterize the genetic heterogeneity of breast cancer. However, identifying novel targets and selecting the best from the sizeable lists of candidate targets is still a key challenge for targeted therapy, largely owing to the lack of economical, efficient and systematic discovery and assessment to prioritize potential therapeutic targets. Here, we describe an approach that combines the computational evaluation and objective, multifaceted assessment to systematically identify and prioritize targets for biological validation and therapeutic exploration...
February 24, 2017: Genes
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