Illumina has sued Qiagen, alleging that the company's GeneReader next-generation sequencing instrument infringes on a patent Illumina holds related to sequencing-by-synthesis technology, according to documents filed with the US District Court of the Northern District of California.

Illumina alleges that Qiagen's GeneReader infringes on US Patent No. 7,566,537, titled "Labelled Nucelotides," which describes a method of labeling nucleotides as part of the sequencing-by-synthesis technology underlying Illumina's instruments.

In its suit, Illumina alleges that Qiagen willfully infringed and is therefore entitled to a damages award three times the amount found by the court.

The lawsuit stems from a previous dispute between Illumina and Intelligent Bio-Systems and Columbia University, before Qiagen acquired Intelligent Bio-Systems.

The university originally sued Illumina in 2012, claiming the firm infringed on patents it had licensed to IBS. When Qiagen acquired IBS later that year, it took on that lawsuit. Subsequently, Illumina countersued IBS, claiming IBS infringed on several of its patents.

In a research note, William Quirk, senior research analyst at Piper Jaffray, wrote that while patent infringement lawsuits are hard to predict, the fact that Illumina prevailed in the inter partes review increases its odds of winning the suit against Qiagen. If Illumina does win the suit, Quirk noted that Qiagen would likely "need to drastically alter the internals of GeneReader and/or remove the product from market."