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Affymetrix's Wings Gets SNPed

By Jim Chen et al.

Sometimes a single nucleotide variant among the thousands that make up a typical gene can indicate significant abnormality in a patient. These needles in genomic haystacks, called "Single Nucleotide Polymorphisms", or "SNPs", can be not only medically useful, but quite lucrative to medical diagnostic companies as well.

In 1999, Biologists John Landers, Barbara Jordan, David E. Housman, and Alain Charest files "method[s] of genotyping...based on the use of single nucleotide polymorphisms (SNPs) to perform high throughput genome scans." The methods apparently invented by Lander et al. allowed high-throughput screening of patients' genomes for SNPs relevant to diseases. They assigned to the Massachusetts Institute of Technology ("MIT") their patent, United Patent Number 6,703,228 (the "'228 patent"), claiming, for example:

Claim 1. A method for detecting the presence or absence of a single nucteotide polymorphism (SNP) allele in a genomic DNA sample, the method comprising:

preparing a reduced complexity genome (RCG) from the genomic DNA sample, wherein the RCG is a randomly primed PCR-derived RCG, and
analyzing the RCG for the presence or absence of a SNP allele.

Affymetrix is a California company that sells microarrays, which are devices capable of testing large numbers of genes for the presence of particularly indicative SNPs. On July 1, 2008, MIT and E8 Pharmaceuticals sued Affymetrix for infringing the '228 patent, engaging the services of Wiley Rein, the D.C. law firm that won a patent infringement settlement of more than half a billion dollars from BlackBerry-maker, Research In Motion. Affymetrix previously lost an interference proceeding in the United States Patent & Trademark Office ("USPTO") contesting Lander et al.'s claim to have been the first inventors of these methods, and stands to suffer huge damages should it be found to infringe the '228 patent.

Affymetrix has previously doubted the validity of many so called "gene" patents, a position that dovetails nicely with the company's strong desire not to be forced to license the many existing SNP patents one by one. Now, the company is being sued not on specific SNP patents, but a patent that claims methods of detecting those SNPs. Interestingly, if Affymetrix extends its previous arguments about unpatentability to include these methods, the company's own history of filing patent applications on very similar technologies - including an application that challenged the rightful ownership of the methods claimed in the '628 patent - is likely to smell a tad fishy.

Full post as published by Biolaw Blog on July 23, 2008 (boomark / email).