ABL/Stanford Dispute

3. ABL’s lawsuits vs me and Stanford University

  • In December 2008, ABL filed a lawsuit against Stanford University for breach of contract and against me for “inducing a breach of contract”, “negligent interference with prospective business advantage”, and “defamation.”
  • In March 2009, all charges against Stanford were dismissed after Stanford paid ABL an undisclosed amount of cash. But in April 2009, ABL revised their lawsuit naming me as the sole defendant. (Documents Page)
  • In June 2009, ABL withdrew their lawsuit against me after the following settlement agreement was reached. The settlement conditions included (i) issuing the following joint statement and (ii) providing a link to ABL’s Response to the HarmfulPatents website.


"ABL has dismissed its lawsuit against Dr. Shafer. According to ABL, 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 U.S. Patent Nos. 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. Dr. Shafer remains committed to the reexamination of the ‘786 and ‘988 patents. 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 described above."

1. US Patents 6,081,786 (’786) and 6,188,988 (’988)

  • Patents ‘786 and ‘988 describe the “invention” of using computers to help physicians make treatment decisions. Both patents were continuations of single patent filed in 1998 by TherapyEdge, a spin-off of the North Carolina-based company Triangle Pharmaceuticals.

  • In 2000, the PTO patent examiners Emanual Todd Voeltz and John W Hayes awarded all 66 claims of the the ’786 patent claiming “The specific allowable feature, which distinguishes the present invention over the prior art is the generation of a ranked listing of available therapeutic treatment regimens for the patient.”
  • In 2001, the same patent examiners awarded all 66 claims of the ‘988 patent which is nearly identical to the ‘786 patent except for the fact that it does not require the “the generation of a ranked listing of available treatment options”.
  • By contrast, the European Patent Office rejected every single claim of the European counterpart application stating that the claims were obvious and lacked any inventive steps.
  • In 2004, Advanced Biological Laboratories (ABL) acquired majority control of TherapyEdge and issued the following press release :


"Control of these patents was at the heart of our business strategy. We believe the patents will prove seminal to the diagnosis and treatment of most chronic diseases. The patents broadly cover the computer analysis of multiple databases which lead to a report meant to guide physicians towards the optimal therapy for a given patient. Historically, such reports were principally associated with the treatment of HIV, but we envision that eventually the diagnosis and treatment of most chronic diseases will fall under the claims of these patents as well. We intend to widely license the patents to diagnostic companies, diagnostic service providers and therapeutic manufacturers."


  • In 2004, ABL sued Hoffman La Roche, Virco Laboratories, Applera, Celera Diagnostics, and Abbott Laboratories for patent infringement. The lawsuits are voluntarily withdrawn for unstated reasons. In 2007, ABL sued in the Eastern District of Texas. (Documents Page)

4. My petitions to US Patent and Trademarks Office (PTO) to invalidate the ‘786 and ‘988 patents

  • In October 2008, I petitioned the PTO to reexamine and invalidate the ABL patents asserting that the patents were broad and obvious and that an extensive amount of prior art was not considered by the PTO when it issued the patents.(Documents Page)
  • Although the ‘786 and ‘988 patents were nearly identical, and although the arguments for invalidity were also nearly identical, Deandra Hughes, the patent examiner assigned to review the requests decided to review seven of the 14 substantial new questions of patentability (SNQs aka prior art) for the ’786 patent but only one of the 14 SNQs for the ‘988 patent. (Documents Page)
  • By rejecting most of the SNQs, Examiner Hughes radically constrained the scope of the reexaminations. However, because Hughes accepted at least one SNQ in each reexamination, under Patent Office rules, Hughes decision could not be petitioned to her superiors within the PTO.
  • Examiner Hughes’ actions had an additional significant negative effect on my ability to challenge the ‘988 patent — I had undertaken an “inter partes” reexamination of the ‘988 patent because such an approach affords the reexamination requester additional procedure, including an appeal to judicial authorities (this procedure was unavailable for the ‘786 patent because it issued before the inter partes reexamination procedure had been added to the statute). By rejecting 13 of 14 SNQs at the outset of the ‘988 reexamination, Hughes prevented the prior art associated with these SNQs from being considered by the Board of Patent Appeals or the U.S. Court of Appeals for the Federal Circuit in an appeal.
  • In June 2009, Hughes upheld all 132 claims of the ‘786 and ‘988 patents, making the single argument that none of the prior art she reviewed described an expert medical system with three “distinct knowledge bases”. With her decision, Hughes — whose only previous patent experience has been in the areas of optical systems and electrical communications — also ignored the assessment of the European Patent Office which stated in its rejection of the ABL patents that the precise manner in which knowledge is structured in an expert system is strictly a matter of of organizational convenience and is not an “invention”.
  • In July 2009, I submitted two additional reexamination petitions, one for the ’786 and one for the ‘988 patent, containing 23 additional SNQs providing even more prior art comprising numerous medical expert systems utilizing multiple knowledge sources (Documents Page). The petitions argued that the supposed distinguishing feature of exactly “three distinct knowledge bases” could not be considered an invention because the elusive terms “distinct” and “knowledge bases” were not even defined in the ‘786 and ‘988 patents. With this second set of reexamination petitions, Ted Shortliffe, the creator of the MYCIN expert system and the president of the American Medical Informatics Association, submitted an unpaid sworn declaration stating that the ‘786 and ‘988 patents contained no advance over MYCIN or over many other medical expert systems that were developed years prior the filing of the ‘786 and ‘988 patents.
  • However, once again, examiner Hughes rejected the majority of my SNQs at the outset and in December 2009 upheld all 132 claims of the ‘786 and ‘988 patents. She also discounted the significance of Professor Shortliffe’s declaration, despite his eminent position in the field. (Documents Page)
  • In April 2010, I filed an Appeal with the PTO seeking that Examiner’s Hughes’ decisions with respect to the ’988 patent be reviewed by a USPTO appeals court judge. In July 2010, the PTO rejected the appeal claiming it was submitted one week late. (Documents Page)
  • In June 2010, I filed additional documents for the ’786 and ’988 patents each containing one SNQ (Documents Page). As expected these were rejected by Examiner Hughes. However, because these petitions each contained a single SNQ, Hughes was forced to reject the re-examination petitions in their entirety allowing me for the first time to petition the Director of the Central Reexam Unit of the PTO. These petitions were filed in October 2010. (Documents Page)
  • In June 2011, Director Irem Yucel refused to assess the manner in which the first two reexams for ’786 and ’988 were handled and rejected both petitions dealing with the third pair of reexams (Documents Page).
  • Although the ’786 and ’988 have not yet been invalidated, the scope of these patents has been dramatically and irrevocably narrowed as a result of the PTO arguments made in response to my reexam efforts. In September 2011, I asked the attorney handling the reexams to summarize the progress we have made.

2.Cross-licensing agreement between Stanford University legal counsel and ABL

  • In 1999, I started a free, online HIV Drug Resistance Database (HIVDB) for scientists developing new HIV drugs and clinicians interpreting HIV drug resistance tests. HIVDB contains curated HIV drug resistance data from published papers, the GenBank sequence database, and my laboratory’s research. HIVDB receives data contributions from scores of medical researchers. It receives funding from the NIH and multiple pharmaceutical and diagnostic companies. The website contains interactive programs for analyzing HIV sequences. It is used more than 100,000 times per month by individuals from 100 countries.
  • In early 2007, ABL approached Stanford University’s Office of Technology Licensing (OTL) claiming that the HIV Drug Resistance Database infringed the ‘786 and ‘988 patents because it provides online software programs to help researchers and clinicians interpret HIV-1 drug resistance information.
  • OTL hired the law firm of Morrison & Foerster to investigate ABL’s claims. Shantanu Basu, a Morrison & Foerster attorney, evaluated ABL’s patents and informed me that the HIV Drug Resistance Database did not infringe the ABL patents. In October 2007, Stanford University sued ABL for a Declaratory Judgment that the HIVDB does not infringe the ABL patents and that Stanford has sufficient grounds to seek patent invalidation (Documents Page). According to OTL senior associate Luis Mejia, ABL was so concerned that Stanford’s lawsuit would lead to the invalidation of their patents that ABL was “going to walk away”.
  • However, in March 2008, without my knowledge, Stanford University’s legal counsel signed a cross-licensing agreement with ABL. According to the agreement, Stanford obtained immunity from ABL for the use of the HIV Drug Resistance Database at Stanford University Hospital and in return ABL licensed a family of contentious Stanford patents. Specifically, Stanford University legal counsel was suing Roche Molecular Systems for $200 million claiming that Roche was infringing the very same patents that ABL cross-licensed in the Stanford-ABL agreement.
  • The Stanford-ABL agreement stipulated that I would place a statement on the HIV Drug Resistance Database that would “put the HIV community on notice about ABL’s patents”. However, I did not agree to place ABL’s statement on the HIVDB website because many physicians worldwide rely on the database to obtain information about drug-resistance mutations in viruses from patient samples. By providing commercial-use immunity only to Stanford University Hospital the agreement gave the appearance of sanctioning future ABL lawsuits against non-Stanford affiliated laboratories.
  • When President John Hennessy was informed of the Stanford-ABL agreement, his initial response was: “Based on the brief description of the patent, it would seem that research Stanford did and published 30 years ago, including Mycin, would predate the patent. We do not give in to patent extortion; we also don’t, as a general rule, seek to fix the problems of the patent office.” In a subsequent conversation, Hennessy stated the “U.S. Patent Office is broken” and that the Stanford-ABL agreement was solely a “university business decision.”

5. Stanford University Provost John Etchemendy’s public apology and statement of support for open access to the HIV Drug Resistance Database

  • In June 2009, at the advice of several senior Stanford faculty, I filed a grievance with the Stanford University Advisory Board arguing that the two agreements Stanford University’s legal counsel made with ABL were not in the public interest and violated University policies on academic freedom, ownership of intellectual work, and university licensing procedures.
  • The Advisory Board appointed an investigator who conducted extensive interviews and reviewed the documents and emails relevant to this dispute. In April 2010, I received a redacted version of the Advisory Board’s report which stated that “The board judged that it was a mistake to enter into the binding agreement with ABL without consulting Professor Shafer and expressed deep concerns about some of the subsequent actions taken by the University to comply with the agreement. The board concluded that these actions were inconsistent with the general principles of academic freedom.”
  • I subsequently met with the Provost who issued the following apology at the June 2010 Senate Faculty Meeting.


"Earlier this year, Stanford Provost John Etchemendy asked the university’s faculty Advisory Board to investigate an appeal brought to him by Professor Robert Shafer, a faculty member in the Department of Medicine. The Advisory Board concluded that that university made a mistake in not consulting with Professor Shafer before agreeing to a legal settlement involving the HIV database Web site created by Professor Shafer, an open and accessible resource used by clinicians and researchers worldwide studying treatments for HIV.

Provost Etchemendy agrees with the Advisory Board’s conclusion. The provost determined that the university committed a serious procedural error when it did not consult with Professor Shafer prior to entering into an agreement with Advanced Biological Laboratories. In 2007, ABL threatened the university with litigation over alleged patent infringement by the HIV Web site. Although in settling with ABL, it was the intent of the university to protect Professor Shafer’s valuable research and maintain broad access to the content of the Web site, it should not have done so without consulting and involving him in the process.

The HIV Drug Resistance Database was started by Professor Shafer in 1998 and contains data contributed by medical researchers around the world. Funded by the NIH, multiple pharmaceutical and diagnostic companies, and Stanford, the database is used more than 100,00 times each month by clinicians and researchers–-representing more than 100 countries–-who are involved in HIV drug resistance testing and developing drugs to combat HIV.

Stanford University strongly supports the work done by Professor Shafer to develop the HIV database and affirms its ongoing value to the scientific community in diagnosing and treating HIV around the globe. The university wants to reassure scholars and scientists who have contributed content or provided financial support to the HIV database that Stanford endorses open access to the data. The HIV database represents the best of public service scholarship and research at the university, and as such, Provost Etchemendy will be providing further research funding in support of expansion of the database.

Provost Etchemendy has apologized for the error before the university’s Faculty Senate and has indicated that the university will establish a process to ensure that faculty members are consulted on legal settlements that directly impact their research. He has asked the Advisory Board to review university practices related to this issue and will recommend that Professor Shafer advise the Board on this issue."