See Which Patents are in Play in Affymetrix vs. Illumina | GenomeWeb

In Affymetrix's July 26, 2004 lawsuit against Illumina, the firm alleged in US District Court that Illumina has been infringing on six of its patents listed below. Illumina fired back in September of last year, stating that they are not infringing or that the Affy patents should be invalidated, according to Illumina's attorney, Marc Sernel.

Listed below are the patents in question.

Title: Computer-aided visualization and analysis system for sequence evaluation

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