Back grey_arrow_rt.gif
Stanford Professor Bob Shafer Settles with ABL in HIV Database Legal Spat; Pursues Patent Reexams
  June 22, 2009
By Ben Butkus
Luxembourg's Advanced Biological Laboratories last week settled a defamation lawsuit against a Stanford University professor who claimed that ABL was discouraging physicians from freely using his online database for HIV drug resistance by enforcing its own bioinformatics patents.
The agreement comes approximately three months after ABL and Stanford reached their own settlement in the lawsuit, which ABL filed in December against both the university and the professor, Robert Shafer. In the suit, ABL accused Shafer and Stanford of defamation and of breaching a patent immunity contract Stanford and ABL had previously inked regarding the HIV database.
Despite the settlement, Shafer said this week that he will continue to dispute the validity of ABL's patents with the US Patent and Trademark Office; and that he will maintain a website to draw attention to what he considers detrimental "medical process" patents, using his dispute with ABL as a case study. ABL disclosed details of both settlement agreements in separate statements issued this week.
The legal morass revolved around a pair of patents, US Nos. 6,081,786 and6,188,988, which are owned by ABL (after it purchased them from now-defunct biotech startup Triangle Pharmaceuticals) and pertain to methods of using a computer to guide the selection of therapeutic treatment regimens for known diseases; and the Stanford University HIV Drug Resistance Database, a free online resource for guiding HIV treatment maintained by Robert Shafer, an associate professor of medicine and pathology at the school.
Sometime before October 2007, ABL threatened to sue Stanford because the HIVdb website, which Stanford offered free to the general public, allegedly infringed upon the '786 and '988 patents.
In response, Stanford sued ABL in October 2007 for declaratory relief, claiming that it had sufficient grounds for invalidating the ABL patents based on a previously awarded family of patents - US RE38352; 5,856,086; and 5,631,128 - that the school owned related to using PCR assays to monitor antiviral therapy and make therapeutic decisions to treat HIV patients.
In March 2008, however, Stanford and ABL negotiated an agreement under which neither entity would sue the other for infringement, with the understanding that the HIVdb website could be used for research purposes only, except by Stanford; and that Stanford would place a disclaimer on the database that use of the site did not imply rights under the '786 and '988 patents, particularly for those standing to commercially benefit from use of the database.
According to Shafer, this patent immunity agreement was inked without his knowledge or consent, and he did not agree to the disclaimer, arguing that ABL's patents were overly broad and obvious and that such a disclaimer on the site would discourage its use by any party.
"The implication was that any other commercial lab would have to think twice before they used the database," Shafer told BTW in an interview earlier this month. "Of course the agreement didn't give [ABL] the right to sue those labs, but they always have that right."
The agreement also gave ABL "ammunition," Shafer added, because "it strengthened the non-obviousness of the ABL paten and it weakened a public resource that has been funded by the taxpayer dollars." Although Shafer made his comments earlier this month, this week he told BTW that he stood by them.
In October of last year, Shafer initiated a reexamination of ABL's patents with the USPTO; and at some point, the exact timing of which is unclear, constructed a new website,, which laid out his case against ABL. In response, ABL in December filed its breach of contract and defamation suit against Shafer and Stanford.
Finally, in March, Stanford and ABL settled again, this time for an undisclosed amount of money paid by Stanford in exchange for ABL dropping its suit against the school. Following this, ABL amended its complaint to name Shafer as the sole defendant, and defamation as the primary complaint. ABL did not disclose financial details of the settlement with Stanford.
ABL last week for the first time disclosed details of the original patent immunity and settlement agreements, although documents pertaining to both have been available on
In a statement, ABL said that it "has not and will not seek to shut down Stanford's HIVdb website, nor does it seek to hamper research or non-profit activity. ABL denies such allegations and rumors that have been made about its relations with Stanford, which it believes are based on a misinterpretation of its intentions."
In addition, ABL disclosed that since 2005 it has "actively co-invested [in the database] through an in-licensing agreement with the Stanford Office of Technology Licensing, and is further promoting at its own expense around the world, and paying minimum yearly royalties to OTL on all ABL worldwide sales that are using the licensed HIVdb Drug Resistance Algorithm."
The algorithm referenced in ABL's statement was related to know-how that the company licensed from Stanford and Shafer in 2005 to use in its ViroScorer HIV product for helping doctors tailor therapies for HIV patients based on drug resistance. It is unclear whether ABL's agreement regarding this algorithm came into play in its original communications with Stanford about its possible infringement of the '786 and '988 patents. ABL was unable to be reached for comment.
Shafer told BTW earlier this month that he was "very disappointed that Stanford made [the patent immunity] agreement that compromised a free public resource, and strengthened a patent that many people consider obvious and that has been the cause of several lawsuits."
Prior to its legal row with Stanford and Shafer, ABL had sued several companies for allegedly infringing the same patents, including Hoffman La Roche, Virco Laboratories, Applera, Celera Diagnostics, Abbott Laboratories, SmartGene, and Ameripath. The suits against Hoffman La Roche, Virco, Applera, Celera, and Abbott were dropped for undisclosed reasons. Meantime, ABL settled with Ameripath last year and had its suit against SmartGene dismissed in a Texas court.
In addition, Shafer said that he was also "disappointed for a second time that Stanford settled with ABL independently of me. In some ways, Stanford is bankrolling ABL's continued efforts against me." Shafer made these comments earlier this month, when his negotiations with ABL were ongoing, but he again stood by his quotes this week.
Shafer's disappointment with his employer notwithstanding, last week, under orders from the district court in which the suit was originally filed, ABL and Shafer finally negotiated their own settlement.
Under the terms of the settlement, ABL agreed to dismiss its lawsuit against Shafer, in exchange for Shafer removing from the site certain language that suggested ABL's patents were undeserved and obvious, and that users of the HIVdb site should be concerned about restrictions that ABL might place on the use of the site.
In a statement endorsed by Shafer, ABL said that it "never intended to shut down or adversely impact the HIVdb. To further demonstrate its commitment to the HIV community at large, ABL clarifies that it will not assert its US Patent 6,081,786 and 6,188,988 against any non-profit institution, or any hospital, researcher, or individual doctor that utilizes it in the treatment of HIV." However, the agreement between Shafer and ABL does not preclude him from pursuing a reexamination of the '786 and '988 patents, which he said he continues to do.
"Dr. Shafer remains committed to the reexamination of the '786 and '988 patents," ABL said in its statement. "ABL believes its issued patents will withstand this challenge and plans to continue to defend its intellectual property against unauthorized commercial use, subject to the limitations" it described regarding not-for-profit use.
ABL also said that the USPTO has issued a pair of actions closing prosecution, confirming the patentability of all 66 claims of the '988 patent, "thus closing prosecutions of both the ex parte and inter partes reexaminations of this patent."
However, Shafer told BTW this week that this office action was expected due to a loophole he and his patent attorney discovered in their original reexamination filing; and that they are currently preparing another reexamination request that they believe will eventually render the ABL patents invalid.
As for, Shafer said that his goal now is to modify the site to focus on medical process patents, which he says are a source of many ongoing patent disputes and a general bane of the medical community.
"ABL will be one of the case studies," Shafer said. "I'm not saying that all patents are harmful, but these medical process patents generally are. Hopefully the site will help raise awareness."
  icon paper stack View Older Articles   Back to Top