scholarly journals Genomic medicine: genetic variation and its impact on the future of health care

2005 ◽  
Vol 360 (1460) ◽  
pp. 1543-1550 ◽  
Author(s):  
Huntington F Willard ◽  
Misha Angrist ◽  
Geoffrey S Ginsburg
Keyword(s):  
Health Care ◽  
Large Scale ◽  
New Technologies ◽  
Clinical Medicine ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genomic Medicine ◽  
Genome Project ◽  
Breast Cancer Patients ◽  
Individualized Care

Advances in genome technology and other fruits of the Human Genome Project are playing a growing role in the delivery of health care. With the development of new technologies and opportunities for large-scale analysis of the genome, transcriptome, proteome and metabolome, the genome sciences are poised to have a profound impact on clinical medicine. Cancer prognostics will be among the first major test cases for a genomic medicine paradigm, given that all cancer is caused by genomic instability, and microarrays allow assessment of patients' entire expressed genomes. Analysis of breast cancer patients' expression patterns can already be highly correlated with recurrence risks. By integrating clinical data with gene expression profiles, imaging, metabolomic profiles and proteomic data, the prospect for developing truly individualized care becomes ever more real. Notwithstanding these promises, daunting challenges remain for genomic medicine. Success will require planning robust prospective trials, analysing health care economic and outcome data, assuaging insurance and privacy concerns, developing health delivery models that are commercially viable and scaling up to meet the needs of the whole population.

scholarly journals Genomic Medicine

2016 ◽  
Vol 23 (1) ◽  
pp. 21
Author(s):  
Kremema Star ◽  
Barbara Birshtein
Keyword(s):  
Human Genome ◽  
Human Disease ◽  
Human Genome Project ◽  
Large Scale ◽  
New Technologies ◽  
Genomic Medicine ◽  
Genetic Material ◽  
Genome Project ◽  
The Human Genome Project

The human genome project created the field of genomics – understanding genetic material on a large scale. Scientists are deciphering the information held within the sequence of our genome. By building upon this knowledge, physicians and scientists will create fundamental new technologies to understand the contribution of genetics to diagnosis, prognosis, monitoring, and treatment of human disease. The science of genomic medicine has only begun to affect our understanding of health.

scholarly journals Discovering Distinct Patterns in Gene Expression Profiles

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Li Teng ◽  
Laiwan Chan
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Clustering Methods ◽  
Gene Expressions ◽  
Real Gene ◽  
Large Scale Dataset ◽  
Coexpressed Genes

SummaryTraditional analysis of gene expression profiles use clustering to find groups of coexpressed genes which have similar expression patterns. However clustering is time consuming and could be diffcult for very large scale dataset. We proposed the idea of Discovering Distinct Patterns (DDP) in gene expression profiles. Since patterns showing by the gene expressions reveal their regulate mechanisms. It is significant to find all different patterns existing in the dataset when there is little prior knowledge. It is also a helpful start before taking on further analysis. We propose an algorithm for DDP by iteratively picking out pairs of gene expression patterns which have the largest dissimilarities. This method can also be used as preprocessing to initialize centers for clustering methods, like K-means. Experiments on both synthetic dataset and real gene expression datasets show our method is very effective in finding distinct patterns which have gene functional significance and is also effcient.

CFTR ΔF508 mutation has minimal effect on the gene expression profile of differentiated human airway epithelia

2005 ◽  
Vol 289 (4) ◽  
pp. L545-L553 ◽  
Author(s):  
Joseph Zabner ◽  
Todd E. Scheetz ◽  
Hakeem G. Almabrazi ◽  
Thomas L. Casavant ◽  
Jian Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cystic Fibrosis ◽  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Primary Cultures ◽  
Gene Expression Profiles ◽  
Filter Method ◽  
Tissue Destruction ◽  
Airway Epithelia

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial chloride channel regulated by phosphorylation. Most of the disease-associated morbidity is the consequence of chronic lung infection with progressive tissue destruction. As an approach to investigate the cellular effects of CFTR mutations, we used large-scale microarray hybridization to contrast the gene expression profiles of well-differentiated primary cultures of human CF and non-CF airway epithelia grown under resting culture conditions. We surveyed the expression profiles for 10 non-CF and 10 ΔF508 homozygote samples. Of the 22,283 genes represented on the Affymetrix U133A GeneChip, we found evidence of significant changes in expression in 24 genes by two-sample t-test ( P < 0.00001). A second, three-filter method of comparative analysis found no significant differences between the groups. The levels of CFTR mRNA were comparable in both groups. There were no significant differences in the gene expression patterns between male and female CF specimens. There were 18 genes with significant increases and 6 genes with decreases in CF relative to non-CF samples. Although the function of many of the differentially expressed genes is unknown, one transcript that was elevated in CF, the KCl cotransporter (KCC4), is a candidate for further study. Overall, the results indicate that CFTR dysfunction has little direct impact on airway epithelial gene expression in samples grown under these conditions.

scholarly journals Transcriptome Profiling of Adipose Tissue Reveals Depot-Specific Metabolic Alterations Among Patients with Colorectal Cancer

2019 ◽  
Vol 104 (11) ◽  
pp. 5225-5237 ◽  
Author(s):  
Mariam Haffa ◽  
Andreana N Holowatyj ◽  
Mario Kratz ◽  
Reka Toth ◽  
Axel Benner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Adipose Tissue ◽  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Human Study ◽  
Subcutaneous Fat ◽  
Specific Gene ◽  
Adipose Tissue Depots

Abstract Context Adipose tissue inflammation and dysregulated energy homeostasis are key mechanisms linking obesity and cancer. Distinct adipose tissue depots strongly differ in their metabolic profiles; however, comprehensive studies of depot-specific perturbations among patients with cancer are lacking. Objective We compared transcriptome profiles of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) from patients with colorectal cancer and assessed the associations of different anthropometric measures with depot-specific gene expression. Design Whole transcriptomes of VAT and SAT were measured in 233 patients from the ColoCare Study, and visceral and subcutaneous fat area were quantified via CT. Results VAT compared with SAT showed elevated gene expression of cytokines, cell adhesion molecules, and key regulators of metabolic homeostasis. Increased fat area was associated with downregulated lipid and small molecule metabolism and upregulated inflammatory pathways in both compartments. Comparing these patterns between depots proved specific and more pronounced gene expression alterations in SAT and identified unique associations of integrins and lipid metabolism–related enzymes. VAT gene expression patterns that were associated with visceral fat area poorly overlapped with patterns associated with self-reported body mass index (BMI). However, subcutaneous fat area and BMI showed similar associations with SAT gene expression. Conclusions This large-scale human study demonstrates pronounced disparities between distinct adipose tissue depots and reveals that BMI poorly correlates with fat mass–associated changes in VAT. Taken together, these results provide crucial evidence for the necessity to differentiate between distinct adipose tissue depots for a correct characterization of gene expression profiles that may affect metabolic health of patients with colorectal cancer.

scholarly journals An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Yun Sung Cho ◽  
Hyunho Kim ◽  
Hak-Min Kim ◽  
Sungwoong Jho ◽  
JeHoon Jun ◽  
...  
Keyword(s):  
Large Scale ◽  
New Technologies ◽  
Reference Genome ◽  
Genomic Structure ◽  
Genome Project ◽  
Personal Genome ◽  
Personal Genomic ◽  
Personal Reference ◽  
Scale Population ◽  
Genome Assemblies

Abstract Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity.

scholarly journals Telemedicine and Virtual Reality at Time of COVID-19 Pandemic: An Overview for Future Perspectives in Neurorehabilitation

2021 ◽  
Vol 12 ◽  
Author(s):  
Marta Matamala-Gomez ◽  
Sara Bottiroli ◽  
Olivia Realdon ◽  
Giuseppe Riva ◽  
Lucia Galvagni ◽  
...  
Keyword(s):  
Health Care ◽  
Large Scale ◽  
New Technologies ◽  
Care Center ◽  
Risk Of Infection ◽  
Patient Counseling ◽  
Public Health Response ◽  
Process Flow ◽  
Health Care Center ◽  
Comprehensive Service

In catastrophic situations such as pandemics, patients' healthcare including admissions to hospitals and emergency services are challenged by the risk of infection and by limitations of healthcare resources. In such a setting, the use of telemedicine interventions has become extremely important. New technologies have proved helpful in pandemics as a solution to improve the quality of life in vulnerable patients such as persons with neurological diseases. Moreover, telemedicine interventions provide at-home solutions allowing clinicians to telemonitor and assess patients remotely, thus minimizing risk of infection. After a review of different studies using telemedicine in neurological patients, we propose a telemedicine process flow for healthcare of subjects with chronic neurological disease to respond to the new challenges for delivering quality healthcare during the transformation of public and private healthcare organizations around the world forced by COVID-19 pandemic contingency. This telemedicine process flow represents a replacement for in-person treatment and thereby the provision equitable access to the care of vulnerable people. It is conceptualized as comprehensive service including (1) teleassistance with patient counseling and medical treatment, (2) telemonitoring of patients' health conditions and any changes over time, as well as (3) telerehabilitation, i.e., interventions to assess and promote body functions, activities, and consecutively participation. The hereby proposed telemedicine process flow could be adopted on a large scale to improve the public health response during healthcare crises like the COVID-19 pandemic but could equally promote equitable health care independent of people's mobility or location with respect to the specialized health care center.

Toward an evidence-based toxicology

2006 ◽  
Vol 25 (9) ◽  
pp. 497-513 ◽  
Author(s):  
S Hoffmann ◽  
T Hartung
Keyword(s):  
Test Performance ◽  
Large Scale ◽  
New Technologies ◽  
Clinical Medicine ◽  
Evidence Based ◽  
Use Of Resources ◽  
Testing Strategies ◽  
Mechanistic Understanding ◽  
Traditional Approaches ◽  
Based Medicine

The increasing demands on toxicology of large-scale risk assessment programmes for chemicals and emerging or expanding areas of chemical use suggest it is timely to review the toxicological toolbox. Like in clinical medicine, where an evidence-based medicine (EBM) is critically reviewing traditional approaches, toxicology has the opportunity to reshape and enlarge its methodology and approaches on the basis of compounded scientific knowledge. Such revision would have to be based on structured reviews of current practice, ie, assessment of test performance characteristics, mechanistic understanding, extended quality assurance, formal validation and the use of integrated testing strategies. This form of revision could optimize the balance between safety, costs and animal welfare, explicitly stating and, where possible, quantifying uncertainties. After a self-critical reassessment of current practices and evaluation of the thus generated information, such an evidence-based toxicology (EBT) promises to make better use of resources and to increase the quality of results, facilitating their interpretation. It shall open up hazard and also risk assessments to new technologies, flexibly accommodating current and future mechanistic understanding. An EBT will be better prepared to answer the continuously growing safety demands of modern societies.

scholarly journals Moderate alcohol consumption alters both leucocyte gene expression profiles and circulating proteins related to immune response and lipid metabolism in men

2011 ◽  
Vol 108 (4) ◽  
pp. 620-627 ◽  
Author(s):  
Michel M. Joosten ◽  
Marjan J. van Erk ◽  
Linette Pellis ◽  
Renger F. Witkamp ◽  
Henk F. J. Hendriks
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Lipid Metabolism ◽  
Alcohol Consumption ◽  
Orange Juice ◽  
Large Scale ◽  
Disease Risk ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Moderate Alcohol Consumption

Moderate alcohol consumption has various effects on immune and inflammatory processes, which could accumulatively modulate chronic disease risk. So far, no comprehensive, integrative profiling has been performed to investigate the effects of longer-term alcohol consumption. Therefore, we studied the effects of alcohol consumption on gene expression patterns using large-scale profiling of whole-genome transcriptomics in blood cells and on a number of proteins in blood. In a randomised, open-label, cross-over trial, twenty-four young, normal-weight men consumed 100 ml vodka (30 g alcohol) with 200 ml orange juice or only orange juice daily during dinner for 4 weeks. After each period, blood was sampled for measuring gene expression and selected proteins. Pathway analysis of 345 down-regulated and 455 up-regulated genes revealed effects of alcohol consumption on various signalling responses, immune processes and lipid metabolism. Among the signalling processes, the most prominently changed was glucocorticoid receptor signalling. A network on immune response showed a down-regulated NF-κB gene expression together with increased plasma adiponectin and decreased pro-inflammatory IL-1 receptor antagonist and IL-18, and acute-phase proteins ferritin and α1-antitrypsin concentrations (all P < 0·05) after alcohol consumption. Furthermore, a network of gene expression changes related to lipid metabolism was observed, with a central role for PPARα which was supported by increased HDL-cholesterol and several apo concentrations (all P < 0·05) after alcohol consumption. In conclusion, an integrated approach of profiling both genes and proteins in blood showed that 4 weeks of moderate alcohol consumption altered immune responses and lipid metabolism.

scholarly journals Spatially resolved transcriptomics reveals plant host responses to pathogens

2019 ◽  
Author(s):  
Michael Giolai ◽  
Walter Verweij ◽  
Ashleigh Lister ◽  
Darren Heavens ◽  
Iain Macaulay ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Cell Types ◽  
Complex Model ◽  
Model Systems ◽  
Host Responses ◽  
Plant Host ◽  
Preparation Methods ◽  
Small Areas

AbstractBackgroundThorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present Grid-seq, an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.ResultsWe compare the Grid-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the Grid-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22.ConclusionWe show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.

scholarly journals Network integration of data and analysis of oncology interest

2006 ◽  
Vol 3 (1) ◽  
pp. 45-55
Author(s):  
P. Romano ◽  
G. Bertolini ◽  
F. De Paoli ◽  
M. Fattore ◽  
D. Marra ◽  
...  
Keyword(s):  
Web Services ◽  
Large Scale ◽  
New Technologies ◽  
Workflow Management ◽  
Genome Project ◽  
Management Systems ◽  
Workflow Management Systems ◽  
The Creation ◽  
The Human Genome Project ◽  
Integrate Data

Summary The Human Genome Project has deeply transformed biology and the field has since then expanded to the management, processing, analysis and visualization of large quantities of data from genomics, proteomics, medicinal chemistry and drug screening. This huge amount of data and the heterogeneity of software tools that are used implies the adoption on a very large scale of new, flexible tools that can enable researchers to integrate data and analysis on the network. ICT technology standards and tools, like Web Services and related languages, and workflow management systems, can support the creation and deployment of such systems. While a number of Web Services are appearing and personal workflow management systems are also being more and more offered to researchers, a reference portal enabling the vast majority of unskilled researchers to take profit from these new technologies is still lacking. In this paper, we introduce the rationale for the creation of such a portal and present the architecture and some preliminary results for the development of a portal for the enactment of workflows of interest in oncology.

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