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I enjoyed reading your article on Genaissance Pharmaceuticals and your comparison of it with Variagenics (“Happy Days at the HAP Factory,” March 2001).

In the editorial, (“Your Onus to Opine,” March 2001) you generously praise Genaissance CTO Jerry Vovis and CEO Gualberto Ruaño. It is very kind of you.

In the sidebar, you compare the company with its nearly identical competitor, Variagenics. There is a reason for the similarity: I was the one who introduced these technologies at both Genaissance and Variagenics.

I was the first one to represent Genaissance at the 1997 International Pharmacogenomics Conference in Washington and to present the utility of organizing SNPs and using them as predictors of genetic disorders and drug responses. That day Genaissance, as a pharmacogenomics company, was born from the womb of Bios, a service company in New Haven.

At that time, Dr. Ruaño was not convinced of this approach. He was embracing gene expression analysis. Disappointed, I left for Variagenics.

There, with the encouragement of CEO Fred Ledley, I brought more interesting ideas onto the palette. Sadly, both Fred and I had to go because the investors were apparently not convinced that genetics would work at Variagenics.

Later, Dr. Ruaño, watching the progress made by Variagenics, took the ideas I left behind, developed them with the help of Dr. Clairborne Stephens, and raised a lot of money. Good for them.

This development made Variagenics wake up and return to the model that Fred and I had left behind. Using the same set of ideas, Variagenics also raised money and went public. Both companies went public on the strength of identical platforms.

I must confess, however, that I was only able to introduce these ideas because I was familiar with previous work of researchers in model organisms, demonstrating the utility of organized SNPs in model organisms for making reasonable predictions on the behavior of quantitative traits. Ultimately, the credit goes to them. These traits behave the same from Drosophila to Man.

Raju Govindaraju, Lexington, Mass.

Overlooked Oligos

I feel compelled to drop you a quick email in response to your article “Their Oligos Runneth Over,” (March 2001). I feel we were overlooked in the author’s list of “key competitors in the oligo market.” For years, Integrated DNA Technologies has played a key role in the market, and is considered by many to be a major force in this highly competitive industry.

As a side note, I completely enjoy your magazine and read it faithfully.

Deb Scherer, Director of Marketing & Advertising, Integrated DNA Technologies, Inc.

Golden Path or Dirt Trail?

Nathan Goodman is to be congratulated on his article that points out some of the shortcomings of the human genome assembly known as Golden Path (“The Wicked Truth About Annotated Data,” February 2001). I have seen some additional problems that were brought up by searching this database with vector data. Using the accelerated BLAST method known as Tera-BLAST, I found considerable vector contamination. The affected Chromosomes are 1, 4, 5, 7, 11, 13, 14, 16, 17, 19, and 20. Upon further investigation, I found perfect matches up to 1,300 nucleotides long between the E. coli genome and Golden Path. This indicates that vector cleanup was not done before the assembly process was begun.

Martin Gollery, Bioinformatics TimeLogic Corporation

MUTATED COPY

In the February issue, Colleen Doran was incorrectly identified as a media buyer for Sperling Sampson West. She is an independent contractor with Doran Media Services.

In the March issue, MWG Biotech, which sells the RoboSNP 1600 for automated high throughput SNP analysis, was omitted from our list of genotyping tools.

In the same issue Incyte Genomics, which provides a “Custom SNP Discovery Service,” was omitted from a list of companies that perform SNP services.

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