San Diego-based DNA sequencing company Illumina Inc. has been ordered by a federal judge to pay $115.1 million to Auburn, Wash.-based Syntrix Biosystems Inc. in a patent infringement case.

Illumina was ordered in a federal court in Washington state to pay $96 million in damages, as well as pre-judgment interest of $7.3 million from 2005, supplemental damages of $12 million and an ongoing royalty of 8 percent per infringing sale.

The patent in violation was filed by Syntrix in 1998, and received utility patent status in 1999. Syntrix sued Illumina in late 2010 for patent infringement that had been ongoing since 2000.

Syntrix entered a nondisclosure agreement with Illumina in January 2000, according to court documents, in relation to a “potential business relationship” it would have with the San Diego company. However, soon after the agreement was signed, Illumina filed its own utility patent for a similar technology.

The term of the patent in violation extends to October 2019.

In March, the federal jury found Illumina had infringed on the patent — and this week, the company was ordered to pay hefty fine.

“Our legal action was a hard-fought battle every step of the way, as we insisted that the rights of the individual inventor be fully protected,” John Zebala, Syntrix president and founder, said in a statement. “It should be clear to Illumina and others that the willful disregard of valid intellectual property is unacceptable in the United States.”

— Meghana Keshavan