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Technologies and Approaches

This page contains resources of a more general nature or those that cover multiple approaches for 'omics' applications.  Resources more specifically focused are listed in subfolders under the Technologies section in the navigation panel on the left or the menu at the top of these pages.

Cancer Treatment Gets Personal: An Interactive Poster

Ramaswamy, S & the editorial staff, 2006. Science 312(5777):1162a

Intro. Paragraph

Science, with the assistance of scientific advisor Sridhar  of the Center for Cancer Research, Massachusetts General Hospital, has created a poster to accompany its 26 May 2006 special issue on the new science of cancer. The poster is designed to help readers understand the conceptual framework of the new, patient-centered model of cancer care that is emerging, and how it might ultimately be implemented. This interactive online version of the poster includes additional topics and Web links not covered in the print version, and is available free to all site visitors. (A PDF version of the print poster is available to individual and institutional subscribers to Science.)  There is also a link to related cancer resources printed in Science.

Journal Link

Comments

This poster is a good summary in itself but the interactive website is a very good at illustrating the application of genomics to the clinical aspects of cancer.  The points covered include the technical aspects of cancer diagnosis and staging plus the clinical approaches, both 'classical' and molecular.  The interactive nature of the website allows the viewer to follow one's interest in proceeding through the material.  In addition to the references included in the interactive video the link to cancer resources provide a wealth of documentation and details for the presented material.

Genomic medicine: bringing biomarkers to clinical medicine

Seo, D & Ginsburg, GS, 2005. Curr. Opin. Chem. Biol. 9(4):381-6

Abstract

An important by-product of sequencing the human genome has been the development of a novel 'toolbox' for biomarker discovery and development. Genomic medicine is an emerging discipline in the genome sciences that integrates these tools to interrogate genomic variation in well-defined populations in order to develop predictors of disease susceptibility, progression and drug response. Several important classes of biomarkers result from these analyses which, when translated to clinical medicine and drug development, will have an important impact on human health and disease. This review highlights both the opportunities and challenges in bringing biomarkers into clinical medicine.

Journal Link|  PMID

Comment

Brief description of the biomarker toolbox and listing of promising applications in pharmacogenomics and disease classes. One figure depicts the application to acute coronary syndrome. Tables summarize other potential applications.

Primer on medical genomics. Part III: Microarray experiments and data analysis

Tefferi, A et al., 2002. Mayo Clin. Proc. 77(9):927-940.

Abstract

Genomics has been defined as the comprehensive study of whole sets of genes, gene products, and their interactions as opposed to the study of single genes or proteins. Microarray technology is one of many novel tools that are allowing global and high-throughput analysis of genes and gene products. In addition to an introduction on underlying principles, the current review focuses on the use of both complementary DNA and oligodeoxynucleotide microarrays in gene expression analysis. Genome-wide experiments generate a massive amount of data points that require systematic methods of analysis to extract biologically useful information. Accordingly, the current educational communication discusses different methods of data analysis, including supervised and unsupervised clustering algorithms. Illustrative clinical examples show clinical applications, including (1) identification of candidate genes or pathological pathways (ie, elucidation of pathogenesis); (2) identification of "new" molecular classes of diseases that may be relevant in disease reclassification, prognostication, and treatment selection (ie, class discovery); and (3) use of expression profiles of known disease classes to predict diagnosis and classification of unknown samples (ie, class prediction). The current review should serve as an introduction to the subject for clinician investigators, physicians and medical scientists in training, practicing clinicians, and other students of medicine.

Journal Link | PMID

Comment

Rather thorough description of the types of DNA microarrays, their construction, use and analysis of expression levels. Description of two classic examples of using expression microarray data to classify non-Hodgkin lymphoma and acute leukemia. Description of expression microarray data to distinguish BRAC1 from BRCA2 related breast cancer. Useful figures of the microarray data.

Selection of candidate genes in hypertension

Mein, CA et al., 2004. Methods Mol. Med. 108:107-130

Abstract

Essential hypertension is a common disease with multifactorial etiology affecting up to 10 million individuals in the United Kingdom alone. Current knowledge of the genetic contribution to this trait is restricted to a number of rare variants that produce hypertensive phenotypes in a Mendelian fashion and to genes highlighted by work on blood pressure regulation in rodent models. Recent advances in comparative genomics, genome-wide scans for linkage, transcriptomics, proteomics, and metabolomics allow a systematic approach to the prioritization of candidate genes for hypertension and other complex traits. We review the current state of play in these fields related to hypertension and show, with a particular example, how these data may help target genetic studies in the future

Journal Link | PMID

Comment

A good illustration of how the many types of 'omics' can be used focused to identify the possible genes and pathways involved in hypertension disease conditions.  As such, it reviews and correlates with many aspects of biochemistry, physiology and pharmacology in medical school curricula.