SLA presentation June 10, 2002 Top> Genomics I> Genomics II

Genomics & Bioinformatics II:
 Technologies and lab bench to bedside  
not part of June 10, 2002 presentation

Comments? Questions? Revisions?
  mchitty@healthtech.com

Last revised June 9, 2002 Working draft

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Continuation of Genomics and informatics I: Doing a few of the numbers

Technologies
microarrays: Microarrays (in which nucleic acids representing genes are spotted onto or synthesized on a substrate and then tested against a sample) gauge mRNA levels - and thus gene expression. With these tools, many different genes can be studied, enabling expression patterns to be discerned in, for example, diseased versus normal tissue or in early- stage disease tissue versus late- stage disease tissue. [CHI Microarrays report]

Making new technology work may be easier than using it to discover truth. Roger Brent "Functional genomics: learning to think about gene expression data"  Current Biology 9: R338-R341, 1999. Brent compares microarrays to the microscope and telescope because they "enable observation of the previous unobservable" [transcripts expressed under different conditions in cells, tissues, and organisms].

New technologies often spur scientific advances (and are sometimes overhyped).

Unfamiliar technologies can be confusing for almost everyone.

Technologies overview
See also BioMEMS Biological MicroElectro Mechanical Systems, combinatorial chemistry, integrated genomic technologies, nanoscience, sexy technologies, single molecule detection, tissue engineering   

From bench to bedside:   
predictive pharmacogenomics: The use of an individual’s genomic profile to predict how that individual will respond to certain drugs, enabling a personalized, safer, and more efficient approach to medication. The introduction of cost- effective genotyping, a more supportive stance by the FDA, and progress in identifying markers of adverse drug response have led to a renewed interest in this field. The majority of pharmaceutical companies are now routinely storing samples for genotyping, and a growing number of companies are entering into clinical trials with pharmacogenomic drug/ diagnostic combinations.

-Will pharmacogenomics only increase drug market fragmentation? 
-Create profitable niche markets?
-Prospects for any more blockbuster drugs?
-How soon will we have any answers?
Pharmacogenomics glossary

See also ADME, biomarkers, mechanism of action, metabolic profiling, molecular profiling, personalized medicine, pharmacoproteomics,  predictive genomics, structural pharmacogenomics

diseases: Collections of symptoms and signs (phenotypes) that appear to be similar … Similar clinical phenotypes may have very different underlying mechanisms. As genetic capabilities increase, we will have additional tools to subdivide disease designations that are clinically identical. [Allen D. Roses “Pharmacogenetics and future drug development and delivery” Lancet 355 (9212):1358-61 Apr 15, 2000]  

Evolving definitions: determinism (genetic), diagnosis, genetics, prognosis.

See also behavioral genomics, clinical genomics, genetic enhancement, molecular diagnostics, molecular pathology, 

Are we post-genomic yet?   

In most contexts talk about being "post- genomic" seems a little premature. "Post Mendelian" seems more accurate as we move from an era in which genetics has been rooted in monogenic diseases with high penetrance to a greater awareness (but limited understanding) of polygenic diseases (and traits) often with relatively low penetrance.  (Thanks to Sam Broder, Celera Genomics, speaking at CHI’s Implications of Human Genetic Variation, SNPs, Polymorphisms, Diseases & Treatment meeting, Nov. 1998 for this useful insight.)

Genomics glossary

Useful concepts: biocomplexity, complex, complexity, nonlinear.

Challenges and uncertainties  
The pharmaceutical industry, health professionals, and all of us face enormous challenges in trying to learn about, understand and use emerging genetic and genomic information to make personal (and professional) medical decisions and plans, and to have informed public debate. People seem to be expecting more certainty, but I think, for the foreseeable future, we’ll find that nothing is quite as certain as we’d like to believe.

genetic testing: Until now, government sponsored committees convened to address ‘genetic testing’ have generally limited their definition and their reports to concerns regarding diseases caused by single gene mutations… Another class of ‘genetic tests’ is related to pharmacogenetics, including ... variants or other inherited polymorphic traits that are not diagnostic of disease ... Clear language and differentiation of respective ethical, legal and societal issues are required to prevent inaccurate vernacular usage creating a confused public perception. [Allen Roses “Pharmacogenetics and the practice of medicine” Nature 405: 857-865 June 15 2000] 

Genetic testing glossary

See also family history, genetic discrimination, genetic testing, "good genes", "bad genes", predisposition test

and Ethics

Risk assessment  gets personal.  The Median Isn’t the Message by Steven J. Gould http://www.cancerguide.org/median_not_msg.html  Cancer genomics glossary 

Key points from the working draft Human Genome special issues Feb. 2001

Science's review of "The sequence of the human genome" (J. Craig Venter et al 291: 1304-1352 Feb. 16, 2001) concludes that a "paramount challenge awaits: public discussion of this information and its potential for improvement of personal health ...

• There are two fallacies to be avoided: determinism, the idea that all characteristics of the person are 'hard- wired" by the genome;

• and reductionism, the view that with complete knowledge of the human genome sequence, it is only a matter of time before our understanding of gene functions and interactions will provide a complete causal description of human variability."
  http://www.sciencemag.org/cgi/content/full/291/5507/1304  

Nature's "Initial sequencing and analysis of the human genome" (International Human Genome Sequencing Consortium, 409 (no. 6822:860-914, 15 Feb. 2001) concludes "Finally it has not escaped our notice [a graceful allusion to Crick and Watson's 1953 Nature paper] that

• the more we learn about the human genome, the more there is to explore." and ends by quoting T.S. Eliot's Four Quartets [Little Gidding] "We shall not cease from exploration.

• And the end of all our exploring will be to arrive where we started, and know the place for the first time. http://www.nature.com/nature/journal/v409/n6822/  Clinical genomics glossary  

Doing a few of the numbers Basic genetics & genomics

Back to Genomics I

Back to Taxonomies for librarians SLA June 10, 2002   What are taxonomies?   SLA June 10, 2002presentation. 

Mary Chitty mchitty@healthtech.com  http://www.genomicglossaries.comCambridge Healthtech Institute http://www.healthtech.com