Replies to post #44261 on DNAprint Genomics (DNAG)

[Dnaowner]

Public SNP Group Not So Public
by Kristen Philipkoski
May. 11, 2000 PDT


NEW YORK -- A publicly funded scientific consortium -- intended to ultimately provide drug makers with tools to create custom medications -- has not lived up to promises to publicly disclose all of its research. Patent issues are at the heart of the dilemma.

Lincoln Stein, a member of the SNP Consortium comprised of 10 major pharmaceutical companies and five academic institutions, Wednesday said only fully "mapped" SNPs are released into the public database. About 30 percent of SNP discoveries remain private.











SNP mapping goes a step beyond the Human Genome Project by helping researchers get closer to developing novel diagnostic tests as well as individualized medications. SNPs (pronounced snips) are small variations in each person's genes that determine if they are predisposed to certain diseases and how they will respond to drug treatment.

Stein, part of SNP effort working at Cold Spring Harbor Lab, said the lack of full disclosure resulted from the fear that others would patent the consortium's discoveries.

"Someone could pick up an unmapped SNP and add it to their database and claim they have sufficient utility for a patent," said Stein, speaking on Wednesday evening at the Genome Sequencing and Biology Conference held on Long Island.

Fully mapping a SNP makes it more difficult for a company or researcher to claim to have found a novel use for the gene variation.

Some conference goers seemed puzzled by the reasoning and wondered if the SNP Consortium itself might want to patent SNPs, although the formal goal of the effort is to keep all information in the public domain and disseminate it as quickly as possible.

"The answer was a little vague," said Gregg Helt, chief technical officer at Neomorphic, a genomics company in Berkeley, California.

Of the roughly 3 billion nucleotide pairs -- or "building blocks" of DNA -- in the human genome, 99.9 percent are the same for everyone. The approximately 3 million SNPs that exist occur in the remaining 0.1 percent of the genome, and account for the differences between people.

The 10 companies involved in the SNP Consortium include Wellcome Trust, Bayer, Bristol-Myers Squibb, and Glaxo Wellcome.

"A group of companies that are usually blood enemies of each other," Stein said.

But the consortium believes that it will be cheaper, quicker, and more efficient for researchers to develop a high-density, high-quality genetic map if the companies work together.

The academic centers -- including the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, Washington University School of Medicine, Wellcome Trust's Sanger Centre in the United Kingdom, and the Stanford Human Genome Center in Palo Alto, California -- are handling the identification and analysis of the SNPs.

David Altshuler of the Whitehead Institute said last night that his group has identified some 47,000 unique SNPs, while all of the centers combined have found 146,000 SNPs. That's halfway toward the original goal, but the consortium has since said it could find up to 700,000 by early 2001.

Researchers can learn about diseases by examining SNP maps. By locating SNP patterns in a population of patients who suffer from Alzheimer's disease, for example, researchers can compare them to maps of unaffected populations to determine the genetic variations shared by the affected group. Similar studies can be done for populations who respond poorly to a particular drug.