Re: Good articles on bioinformatics, future medicine, speech interfaces

From: J. R. Molloy (
Date: Fri Oct 26 2001 - 08:56:49 MDT

Yet another article on bioinformatics and future medicine:

Researchers Decode Human Diversity
Correlating genomic variation with drug response requires automation, clinical
data, and a lot of informatics technology.

The most visually impressive feature of Genaissance Pharmaceuticals' New
Haven, Conn., facility is the room filled with rows of Applied Biosystems DNA
sequencers that are always running. However, it's what visitors can't see on
the standard company tours--a nondescript bank of computers tucked in an
out-of-the-way room on the top floor and the software that they run--that
distinguishes the company from the many other outfits setting up sequencing


Keep ahead of the information onslaught "In my experience for biotech in general, workflow or LIMS is a do or die issue," says Windemuth. "You can't do a high-throughput process without reliable data management." To keep track of the data, Genaissance relies on LIMS that they have written and those that are commercially available.

Adds Stephens, "Data management and processing are absolutely crucial. You can imagine getting by with minimal requirements if you are analyzing one gene on a single cohort. But when your throughput is close to a hundred new genes a week, you would be utterly swamped without good LIMS and database management." ---

Pharmacogenomics forecast Judson sees a surge of interest in haplotypes and pharmacogenomics. "When we started in 1997, we were the haplotype company," he says. "Our sales calls tended to focus on teaching people what haplotypes were. Now that the NIH [National Institutes of Health, Bethesda, Md.] has announced they are going to build a haplotype map, and several other companies doing similar things, everyone has agreed that they are the best set of markers to use. That's been a major change over the last year or so."

Most companies now have pharmacogenomics groups, says Judson, and are looking into the technology. GlaxoSmithKline, Research Triangle Park, N.C., whose program is headed by Allen David Roses, senior VP/genetics research, announced plans to have a drug on the market within two years that will have a genetic test associated with it. "They were big drivers behind the SNP Consortium," says Judson, referring to their efforts to create a publicly available SNP map that were funded largely by pharmaceutical companies.

On the diagnostic side, Judson also sees growing interest in SNPs. "Ultimately, if you have these tests done in the doctor's office, someone has to be out there doing the test in a high-throughput way," he says. Quest Diagnostics, one of the largest diagnostics firms, has set up a pharmacogenomics arm to get tests running so that they could be available in their approximately 10,000 sites around the country.

"The genotyping platforms have gotten much more robust, cost has come down, and the number of people that do at least some genotyping has increased," says Judson. "There's a lot of interest all around. There's still a certain amount of skepticism, but everybody feels like they have to play with it."

For more information, contact:

Genaissance Pharmaceuticals

Univ. of Washington Genome Center


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Useless hypotheses, etc.: consciousness, phlogiston, philosophy, vitalism, mind, free will, qualia, analog computing, cultural relativism, GAC, Cyc, Eliza, cryonics, individual uniqueness, ego, human values, scientific relinquishment

We move into a better future in proportion as science displaces superstition.

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