Affymetrix' Wings Get SNPed

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 also quite lucrative to medical diagnostic companies as well.

In 1999, Biologists John Landers, Barbara Jordan, David E. Housman, and Alain Charest filed a patent application claiming "method[s] of genotyping...based on the use of single nucleotide polymorphisms (SNPs) to perform high throughput genome scans." These methods claimed by Lander et al. allow high-throughput screening of patients' genomes for SNPs relevant to diseases. Lander et al. 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 - devices capable of rapidly 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, and engaged the services of Wiley Rein, a D.C. law firm that won a patent infringement settlement of more than half a billion dollars from BlackBerry-maker, Research In Motion. Affymetrix had previously lost an interference proceeding in the United States Patent & Trademark Office ("USPTO") that contested Lander et al.'s claim to have been the first inventors of these methods, and now stands to suffer huge damages should it be found to infringe the '228 patent.

Affymetrix has long been a vocal opponent of 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 on a patent that claims methods of detecting those SNPs. Affymetrix has alleged that claims of the '228 patent are invalid. Where Affymetrix previously argued that it was the rightful owner of '228 patent-like claims, now the company considers such claims - owned by another - to be invalid. The result may exert considerable influence over the future of personal medicine.