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ABI Sues Former Chief Patent Counsel, Solexa Over Ownership of Sequencing-by-Ligation IP

This article has been updated from a previous version to correct the year in which Lynx merged with Solexa.
Applied Biosystems late last month sued its former chief patent counsel and Solexa claiming that it, and not Solexa, owns several patents relating to sequencing-by-ligation, the technology used by its upcoming Agencourt next-generation sequencing system.
In its suit, filed on Dec. 26, 2006, ABI claims that the ex-employee, Stephen Macevicz, filed a patent application while he worked at ABI and failed to assign it to the company, which ABI said he was required to do.
ABI also claims that Macevicz went on to assign the application and the three patents it yielded to Lynx Therapeutics, which acquired Solexa in 2005.
ABI seeks, among other things, damages from Solexa “in an amount to be proven at trial,” punitive damages from Solexa, and injunctive relief, which includes “all necessary steps to restore ownership of the patents [to ABI], including patents that may still be pending or may yet issue based on the application.” The company specified that it “does not seek monetary damages from Macevicz.”
Responding to the suit in a statement three days later, Solexa said that the patents are of little significance to its own next-generation sequencer. The company said the suit is “not material to its current or future business” because its 1G Analyzer sequencing system uses sequencing-by-synthesis, not sequencing-by-ligation.
Solexa also said it “has no plans to use any of the sequencing-by-ligation technologies covered by the patents at issue in the suit,” even though it called one of the patents a “valuable asset” as recently as last March.
According to a Securities and Exchange Commission document filed by Lynx in April 2001, Macevicz joined Lynx in September 1995 as vice president of intellectual property. He served as senior patent attorney and chief patent counsel at ABI between 1992 and August 1995.
The patents in dispute are US Patents No. 5,750,341, No. 5,969,119, and No. 6,306,597, all entitled “DNA sequencing by parallel oligonucleotide extensions.” The patents were granted in 1998, 1999, and 2001, respectively. All three appear to cover sequencing-by-ligation, the approach used by ABI’s Agencourt next-generation sequencer, which the company plans to launch this summer. Macevicz is listed as the sole inventor on the patents, which are all assigned to Lynx Therapeutics.
The patents resulted from a single application, US Patent Application No. 8/424,663, filed on April 17, 1995, that ABI said Macevicz filed in his own name. At that time, ABI claims, he was working for ABI as a patent counsel and did not disclose the patent application to the company.
In the complaint, filed with the Santa Clara County Superior Court in San Jose, Calif., ABI said that its employee invention agreement with Macevicz obliged him to assign to the company any inventions that he made while employed there. Excluded from the agreement were inventions he made on his own time, those not using company resources, and in areas unrelated to ABI’s “actual or anticipated” business, and that did not result from work he performed at ABI. Macevicz was also supposed to disclose inventions he believed were exempted from the agreement to the company, according to ABI.
ABI said it has “information and belief” that he “purported to assign the application and the patents to Lynx.” ABI also claims that Lynx should have known that Macevicz was not entitled to assign it the patents.
According to an SEC filing by Aclara BioSciences in 2002, Macevicz went on to work for GeneProt in 2001 and joined Aclara in 2002.
In 2005, he filed a patent application for ParAllele Bioscience, which was acquired by Affymetrix that year. It is unclear whether he is affiliated with a company at the moment. Reached by phone this week, Macevicz declined to comment for this article.

Solexa said last year its “pioneering developments in the area of bead-based sequencing-by-ligation are valuable assets that provide us with additional technology development options as well as strategic licensing opportunities.”

ABI also did not comment for this article and would not say how significant the three patents are for its business. However, since they cover sequencing-by-ligation, it is likely they have importance for ABI’s next-generation Agencourt sequencer, which uses this approach. According to ABI, the company was “unaware of the application or the patents until March 2006,” two months before it said it was planning to acquire Agencourt Personal Genomics.
Solexa’s recent statement dismissing the patents’ significance for its business contradicts a statement it made last March. At that time, Solexa was granted US patent No. 6,969,488, entitled “System and apparatus for sequential processing of analytes,” which it said belongs to a family of patents on bead arrays that, along with two other patents, one of them US Patent No. 6,306,957, a patent claimed by ABI in its suit, “cover the use of microbeads for sequencing by ligation.”
“We believe our pioneering developments in the area of bead-based sequencing by ligation are valuable assets that provide us with additional technology development options as well as strategic licensing opportunities,” Solexa stated at the time. Solexa declined to comment on this and other aspects of this article.
According to Richard Warburg, an intellectual property lawyer with Foley & Lardner in San Diego who is not affiliated with the suit, disputes like this are settled in the majority of cases.
What is important, he said, is the scope of the employer agreement, a type of agreement that is very common. In California, he said, there are some restrictions on what the employer can lay claim to. Also, certain types of employees who are “employed to invent” — for example scientists — may have more stringent requirements to assign all their inventions to the company than others.
While at ABI Macevicz was employed as senior patent attorney and chief patent counsel. “To some extent you can argue that patent lawyers are hired at least to assist in the inventive process,” said Warburg.
Finally, the position the employee holds in the company plays a role, he said: A CEO has more of a commitment than a technician to assign his inventions to the company, for example.
“You really need to wait until all the facts are out, and that won’t happen until a long time from now, maybe even at trial, to hear the other side’s story,” Warburg said.