Patent Docs

Carnegie Mellon University v. Hoffman-La Roche Inc. (Fed. Cir. 2008)

September 9, 2008

By Donald Zuhn —

On Monday, the Federal Circuit affirmed a finding on summary judgment by the District Court for the Northern District of California that the asserted claims of U.S. Patent Nos. 4,767,708 and 5,126,270 and certain asserted claims of U.S. Patent No. 6,017,745 are invalid, and that the remainder of the asserted claims of the ‘745 patent are not infringed by Defendants-Appellees Hoffmann-La Roche, Inc., Roche Molecular Systems, Inc., Roche Diagnostic Systems, Inc., Roche Biomedical Laboratories, Inc., The Perkin Elmer Corporation, Laboratory Corporation of America Holdings, Roche Diagnostic Corp., Laboratory Corporation of America, and Applera Corp. (Roche). In affirming the District Court’s determination of invalidity and noninfringement, the Federal Circuit concluded that the lower court did err in holding the claims invalid for failure to meet the written description requirement or in performing its infringement analysis.

The patents in suit are related to, inter alia, recombinant plasmids for the enhanced expression of DNA polymerase I (which is encoded by the polA gene), bacterial strains containing such plasmids, and methods for conditionally controlling the expression of DNA polymerase I using such bacterial strains. The claimed plasmids, bacterial strains, and methods seek to overcome a problem that existed in the prior art — namely that bacterial host cells transformed with a plasmid containing the entire polA gene overexpress DNA polymerase I, which is lethal in bacterial host cell. In the claimed plasmids, bacterial strains, and methods, this problem is overcome by removing most or all of the polA promoter such that the cloned polA gene "contains essentially none of or at the most only a portion of the activity of its natural promoter."

In August of 1994, Plaintiffs-Appellants Carnegie Mellon University and Three Rivers Biologicals, Inc. (Carnegie Mellon) brought suit against Roche for patent infringement, asserting that Roche’s recombinant plasmid pLSG5, which can be used to express Thermus aquaticus (Taq) DNA polymerase, infringes the ‘708 and ‘270 patents. In response, Roche filed separate motions for summary judgment of invalidity for lack of written description and noninfringement. The District Court granted Roche’s motion for summary judgment of noninfringement of the ‘708 patent and Roche’s motions for summary judgment of invalidity of the ‘708 and ‘270 patents. With respect to Roche’s motion for summary judgment of invalidity of the ‘708 patent, the District Court concluded that the ‘708 patent lacked an adequate written description under Regents of University of California v. Eli Lilly & Co., 119 F.3d 1559 (Fed. Cir. 1997), since the claims encompass a cloned polA gene from any bacterial source, but the specification only describes plasmids containing the polA gene from Escherichia coli.

In January of 2001, Carnegie Mellon filed a second patent infringement suit against Roche, this time alleging infringement of the ‘745 patent. Roche again moved for summary judgment of invalidity for lack of written description, and the District Court again granted Roche’s motion. Roche also moved for summary judgment of noninfringement under the doctrine of equivalents, and the District Court granted this motion as well.

On appeal, Carnegie Mellon argued that the District Court had erred in granting Roche’s motions for summary judgment of invalidity of the ‘708, ‘270, and ‘745 patents. Carnegie Mellon also argued that the District Court had erred in granting Roche’s motions for summary judgment of noninfringement of the ‘708 and ‘745 patents.

With respect to the issue of invalidity of the ‘708 and ‘745 patents, the Federal Circuit noted that "[t]he appealed claims of the ‘708 patent are directed to recombinant plasmids that contain a DNA coding sequence that is broadly defined, and only by its function, viz., encoding DNA polymerase I," and further, that "the generic claims are not limited to a single bacterial species, but broadly encompass coding sequences originating from any bacterial species." The Court similarly noted that "the appealed claims of the ‘745 patent are broadly directed to recombinant plasmids that contain a DNA coding sequence, again, only defined by function, viz., encoding an enzyme with either DNA polymerase or nick-translation activity," and that "[t]hose claims are also not limited to a single bacterial species, but cover all bacterial species."

In addition, the Federal Circuit observed that at the time of invention, out of thousands of bacterial species, only three bacterial polA genes had been cloned, and only one of these genes had been described in the patents at issue. Moreover, despite the description in the patents that "an important feature of this invention [is] that the cloned polA gene fragment contains essentially none of or at the most only a portion of the activity of its natural promoter," the patents "fail to disclose the nucleotide sequence or other descriptive features for a polA gene (including the promoter sequence) from any bacterial source other than E. coli." As a result, the Federal Circuit concluded that no genuine issues of material fact existed as to whether the written descriptions of the ‘708 and ‘745 patents adequately support the appealed claims, and therefore, the Court affirmed the District Court’s grant of summary judgment of invalidity.

With respect to the issue of invalidity of the ‘270 patent, the Federal Circuit determined that the District Court had erroneously found the asserted claims of this patent invalid under Gentry Gallery, Inc. v. Berkline Corp., 134 F.3d 1473 (Fed. Cir. 1998). In particular, the District Court had found the asserted claims invalid for failure to recite the problem that the invention was intended to solve (i.e., lethality). Citing Cooper Cameron Corp. v. Kvaerner Oilfield Products, Inc., 291 F.3d 1317 (Fed. Cir. 2002), the CAFC noted that it had "not announce[d] a new ‘essential element’ test mandating an inquiry into what an inventor considers to be essential to his invention and requiring that the claims incorporate those elements" in Gentry Gallery. However, the Federal Circuit determined that the asserted claims of the ‘270 patent were nonetheless invalid under Eli Lilly for the same reasons that the ‘708 and ‘745 patents were invalid.

Finally, with respect to the issue of noninfringement, the Federal Circuit noted that its affirmance of invalidity of the ‘708 patent rendered the issue of noninfringement of this patent moot. However, because the validity of the claims of the ‘745 patent that were found to be noninfringed had not been challenged, the CAFC was forced to take this issue up. On appeal, Carnegie Mellon argued that Roche’s pLSG5 plasmid infringed the ‘745 patent under the doctrine of equivalents because the substitution of Taq polymerase for E. coli polymerase was an insubstantial and unimportant change that resulted in an infringing equivalent. In affirming the District Court’s grant of summary judgment of noninfringement, the Federal Circuit determined that to find otherwise would be to vitiate the limitation of the asserted claims which required that the bacterial source of the DNA polymerase be E. coli. In particular, the CAFC stated that "in drafting the claims, the patentees specifically chose to limit claim 4 to a recombinant plasmid where the bacterial source is E. coli," and that Carnegie Mellon "cannot now argue that any bacterial source, including Taq, would infringe that claim."

(In an interesting footnote to the opinion, the CAFC noted that "Taq DNA polymerase was and continues to be integral to the success of [the] polymerase chain reaction ("PCR"), a widely used technique in molecular biology," and that Taq polymerase garnered the title of "Molecule of the Year" from Science in 1993. The Court also noted that "[w]hile we reach our decision irrespective of those facts, we readily can see why appellants have attempted to broaden the scope of their claims beyond the E. coli species disclosed.")

Carnegie Mellon University v. Hoffman-La Roche Inc. (Fed. Cir. 2008)
Panel: Circuit Judges Lourie, Bryson, and Prost
Opinion by Circuit Judge Lourie
In re Swanson (Fed. Cir. 2008)

September 8, 2008

By Kevin E. Noonan —

Re-examination, whether ex parte under 35 U.S.C. § 302-307 or inter partes under 35 U.S.C. § 311-318, is a procedure intended to provide an alternative to patent litigation, which Congress characterized as being expensive and inefficient in passing legislation establishing these two routes of post-grant challenge (see H.R. Rep. No. 107-120 (2002)). Perhaps unexpectedly, both avenues have been increasingly used during litigation, as a way to limit the scope of asserted claims, invalidate patents-in-suit altogether, and provide leverage towards settlement. In some instances, re-examination requesting defendants have been able to obtain a stay in the underlying litigation pending completion of Patent Office review, although this is far from being the general or even a frequent occurrence.

The scope of re-examination has also been expanded by statute, specifically a revision meant to overturn the Federal Circuit’s decision in In re Portola Packaging Inc., 110 F.3d 786 (Fed. Cir. 1997). In that case, the Court found it improper to base the existence of a substantial new question of patent validity on a reference that had been considered during initial ex parte examination. In Portola Packaging, although the reference was the same, the ground of rejection asserted was different, being an obviousness rejection based on a combination of the previously-considered reference and a newly-applied reference. Congress disagreed with this interpretation of the statute (H.R. Rep. No 107-120, at 2):

[T]he appropriate test to determine whether a "substantial new question of patentability" exists should not merely look at the number of references or whether they were previously considered or cited but their combination in the appropriate context of a new light as it bears on the question of the validity of the patent.

In effectuating this change, amended section 303(a) as follows (the amendment appears in italics):

(a) Within three months following the filing of a request for reexamination under the provisions of section 302 of this title, the Director will determine whether a substantial new question of patentability affecting any claim of the patent concerned is raised by the request, with or without consideration of other patents or printed publications. On his own initiative, and any time, the Director may determine whether a substantial new question of patentability is raised by patents and publications discovered by him or cited under the provisions of section 301 of this title. The existence of a substantial new question of patentability is not precluded by the fact that a patent or printed publication was previously cited by or to the Office or considered by the Office.

The extent to which "old" art qualifies in support of establishing a substantial new question of patentability sufficient to declare an interference was further clarified on Thursday, when the Federal Circuit issued its decision in In re Swanson. Swanson was the result of a re-examination requested by a litigant, Syntron Bioresearch Inc., that had failed to establish invalidity as an affirmative defense in a patent infringement lawsuit brought by the ‘484 patent’s licensee, Abbott Laboratories (Abbott Labs. v. Syntron Bioresearch, Inc., No. 98-CV-2359 (S.D. Cal. Oct. 12, 2001)). The judgment of the trial court was affirmed by the Federal Circuit (Abbott Labs. v. Syntron Bioresearch, Inc., 334 F.3d 1343 (Fed. Cir. 2003)). Not to be deterred, however, Syntron filed a request for re-examination of the ‘484 patent, which was granted by the U.S. Patent and Trademark Office as Reexamination Serial No. 90/006,785.

The patent-in-reexamination, U.S. Patent No. 5,073,484, claimed methods for analyzing a biologically-relevant analyte present in biological fluids such as "milk, blood, urine" and the like, wherein a bound reactant is immobilized on a test strip in "reaction zones," and the analyte-containing fluid is motivated through the strip. The presence of an analyte specific for a reactant in a reactant zone is detected by a reaction, preferably a color change that can be seen in each of the zones on the strip. Claim 22 of the ‘484 patent was specifically at issue in the re-examination:

22. A method for analysis of an analyte which is a member of a ligand-anti-ligand binding pair in a test solution comprising the steps of:
(a) providing a non-diffusively immobilized reactant in each of one or more reaction zones spaced successively along a flow path defined by a liquid permeable medium, wherein said reactant is the other member of said binding pair and is capable of binding with the analyte to form a predetermined product;
(b) flowing said solution along the medium and sequentially through the reaction zone(s); and
(c) detecting the presence of analyte, said reactant or said predetermined product in the reaction zone(s), wherein the number of zones in which detection occurs is related to the presence [sic] of analyte solution.

Three dependent claims, reciting detection by a detectable chemical moiety (claim 23), an enzyme (claim 24), or a radioisotope (claim 25) were also at issue.

Several prior art references were asserted against the claims of the ‘484 patent, including one, U.S. Patent No. 4,094,647 ("Deutsch") that had been considered during ex parte examination and had been asserted in support of Syntron’s failed attempt to establish that the ‘484 patent was invalid at trial. The Patent Office in the re-examination rejected claims 22-25 as being anticipated by the Deutsch patent, a determination affirmed by the Board and challenged by Abbott in the appeal. In addition to affirming the Examiner’s rejection of these claims under 35 U.S.C. § 102(b), the Board also rejected the patentee’s contention that reexamination was improper because the Deutsch reference could not raise a substantial new question of patentability because it had been before the Examiner during ex parte examination. The reference did raise a substantial new question of patentability, according to the Board, "because it was not cited in regard to the presently rejected claims and it was not relied upon for the same reason the examiner now relied upon it."

The Federal Circuit limited its review to this last question, since the Board’s determination based in alternative prior art was not challenged by the patentee. In an opinion by Judge Gajarsa, joined by Judges Lourie and Bryson, the Court also rejected the patentee’s argument that the Patent Office was precluded from declaring a re-examination based on the Deutsch reference. The Court characterized this case a "case of first impression," since the scope of available prior art in re-examination had not been considered since Congress amended the statute to overturn Portola Packaging.

The opinion first considered the effect of the District Court decision that the third party re-examination requestor had not established that the claims were invalid over the Deutsch reference. The CAFC rejected the patentee’s contention that the District Court decision had any effect on the question of whether Deutsch could be used to establish a substantial new question of patentability, citing the language of the statute itself, the legislative history, and the "different purposes underlying reexamination and federal court proceedings." First, the Federal Circuit turned to the newly-added language of the amendment, which was focused on art previously cited to or considered by the Patent Office and does not include any art previously cited in court proceedings. The legislative history was in agreement, according to the Court, because it suggested that Congress was solely interested in how these issues were to be considered by the Office and not in civil litigation. This interpretation was consistent with the statutory mandate that re-examination be performed using the same standards as the initial ex parte examination. This included a lack of any presumption of validity, a preponderance of the evidence burden of proof, and giving claim terms the broadest possible interpretation, both features of Patent Office examination that distinguish it from litigation. Even in the context of civil litigation, "a prior holding of validity is not necessarily inconsistent with a subsequent holding of invalidity," according to the opinion, citing Stevenson v. Sears Roebuck & Co., 713 F.2d 705, 710 (Fed. Cir. 1983), "and is not binding on subsequent litigation or PTO reexaminations," citing Ethicon, Inc. v. Quigg, 849 F.2d 1422, 1429 and n.3 (Fed. Cir. 1988). Indeed, the CAFC cited Ethicon for the proposition that "if the district court determines a patent is not invalid, the PTO should continue its reexamination because, of course, the two forums have different standards of proof for determining invalidity" (see Ethicon, 849 F.2d at 1428-29). The Court concluded that the PTO’s position was correct, because otherwise Congressional intent could be "thwarted" by a litigant’s failure to sustain its burden of establishing invalidity by clear and convincing evidence, which is too high a standard for Patent Office action. Since this heightened burden was a consequence of the presumption of validity, it would be improper to effectively transfer this burden to Patent Office proceedings directed to whether a patentee’s claims rightfully enjoyed the presumption.

The fact that the Deutsch patent was considered during ex parte examination resulting in the ‘484 patent was also not sufficient to preclude a Patent Office finding of a substantial new question of patentability, according to the Federal Circuit. Such a conclusion would be clearly contrary to the express terms used in the statute and clearly be contrary to the intent of Congress to overrule the Portola Packaging decision, in the Court’s view. The CAFC also outlined the contours of what could not be used to raise a substantial new question of patentability: "[a]s was true before the amendment, an ‘argument already decided by the Office, whether during the original examination or an earlier reexamination’ cannot raise a new question of patentability," citing H.R. Rep. No. 96-1307 and In re Recreative Technologies Corp., 83 F.3d 1394, 1396-97 (Fed. Cir. 1996). The Court cites the context of prior Patent Office consideration as being one dispositive question: "the PTO should evaluate the context in which the reference was previously considered and the scope of the prior consideration and determine whether the reference is now being considered for a substantially different purpose," citing H.R. Rep. No. 107-120, at 3.

Since the Federal Circuit considered such contextual questions to depend on a consideration of "if and how the examiner used the reference in making his initial decisions" and that this constituted a question of fact, it reviewed for substantial evidence. Using this standard, the CAFC found that the Board had substantial evidence supporting its determination that the Deutsch reference, in the context of the reexamination, raised a substantial new question of patentability (the ultimate question remaining one of law reviewed de novo). The Court said that the Board properly considered that Deutsch had been considered no more than a secondary reference during initial examination, and was not specifically applied to the pending claims. The difference in how the Deutsch reference was used in the reexamination, as a primary reference asserted as anticipating claims 22-25, was enough that it raised a substantial new question of patentability that had not been considered during initial examination.

Although the "context" requirement is also not expressly found in the statutory language, its effects are consistent with the use of previously-considered prior art in Portola Packaging, insofar as the art was used in both Portola and here to raise a patentability issue not previously considered by the Examiner. This decision further expands the capacity for art, previously cited or not, to be used to support a reexamination request, and makes it easier for a third party, especially a litigant, to use the reexamination statute to her advantage. Arguably, that was exactly what Congress had in mind.

In re Swanson (Fed. Cir. 2008)
Panel: Circuit Judges Lourie, Bryson, and Gajarsa
Opinion by Circuit Judge Gajarsa
Court Report

September 7, 2008

By Sherri Oslick —

About
Court Report: Each week we will report briefly on recently filed
biotech and pharma cases, and a few interesting cases will be selected
for periodic monitoring.

Glaxo Group Ltd. et al. v. Lupin Ltd. et al.
1:08-cv-00551; filed August 29, 2008 in the District Court of Delaware

Infringement of U.S. Patent No. 5,859,021 ("Antiviral Combinations," issued January 12, 1999) following a Paragraph IV certification as part of Lupin’s filing of an ANDA to manufacture a generic version of Glaxo’s Combivir® (lamivudine and zidovudine, used in the treatment of HIV-1 infection). View the complaint here.

Teva Pharmaceutical Industries Ltd. et al. v. Glenmark Generics Inc., USA et al.
3:08-cv-04355; filed August 29, 2008 in the District Court of New Jersey

Infringement of U.S. Patent Nos. 6,699,997 ("Carvedilol," issued March 2, 2004) and 7,126,008 (same title, issued October 24, 2006) based on Glenmark’s sale and/or manufacture of a generic version of GSK’s Coreg® (carvedilol, used to treat congestive heart failure). View the complaint here.

Pfizer Inc. et al. v. Impax Laboratories, Inc.
2:08-cv-04356; filed August 29, 2008 in the District Court of New Jersey

Infringement of U.S. Patent Nos. 5,382,600 ("3,3-Diphenylpropylamines and Pharmaceutical Compositions Thereof, issued January 17, 1995), 6,630,162 ("Pharmaceutical Formulation and Its Use," issued October 7, 2003), and 6,770,295 ("Therapeutic Formulation for Administering Tolterodine with Controlled Release," issued August 3, 2004) following a Paragraph IV certification as part of Teva’s filing of an ANDA to manufacture a generic version of Pfizer’s Detrol LA® (extended release tolterodine tartrate, used to treat overactive bladder). View the complaint here.

Teva Pharmaceuticals USA, Inc. et al. v. Sandoz, Inc. et al.
1:08-cv-07611; filed August 28, 2008 in the Southern District of New York

Infringement of U.S. Patent Nos. 7,199,098 ("Copolymer-I Improvements in Compositions of Copolymers," issued April 3, 2007), 6,939,539 (same title, issued September 6, 2005), 6,054,430 (same title, issued April 25, 2000), and 6,620,847 (same title, issued September 16, 2003) following a Paragraph IV certification as part of Sandoz’s filing of an ANDA to manufacture a generic version of Teva’s Copaxone® (glatiramer acetate injection, used for the reduction of frequency of relapses in patients with relapsing-remitting multiple sclerosis). View the complaint here.
New Attack on Patenting in The New York Times

September 7, 2008

By Kevin E. Noonan —

The New York Times seems to have an unending supply of pundits willing to support its anti-patent agenda, as has been noted on this blog before (see below). The latest example is an article in this Saturday’s paper, entitled "When Academia Puts Profit Ahead of Wonder," by Janet Rae-Dupree. Once past its precious and naïve title, it evinces the same patent animus and the same degree of ignorance about the issues and the stakes behind them.

The piece is ostensibly about the Bayh-Dole Act, passed under the Carter Administration to permit, for the first time, inventors working in U.S. universities and funded by Federal grant monies to apply for patents on their inventions. The program is generally accepted to be a success, providing an alternative source of licensing revenue for universities and "the fire of interest" spurring innovation. But pundits, academic and otherwise, rarely achieve prominence affirming the status quo, and expectedly the success of the Bayh-Dole regime has engendered critics. The critics’ point is that the pursuit of profit has somehow stifled the pursuit of pure science and sullied the motivations of its academic practitioners.

To quote Ms. Rae-Dupree from another context, "Balderdash!" Unmentioned in the piece is the context under which Bayh-Dole was enacted. Before patent protection was available, U.S. academic science, funded by U.S. taxpayers, represented unpaid-for research and development for corporations, many of them from abroad. At least a portion of the American R&D fueled the economic miracle economies of Europe and Asia during the late 1960’s and 1970’s, unwittingly aiding and abetting competition by these economies for American jobs and technology. This trend turned around in the 1980’s, as Bayh-Dole and the creation of the Court of Appeals for the Federal Circuit strengthened patent protection for U.S. inventors. The consequence: a U.S. biotechnology sector that promoted the ascendance of U.S. pharmaceutical companies enjoyed until recently, as well as innovation in the telecommunications and computer fields. (If there is any doubt about the importance of protecting innovation, recall that twenty years ago everyone had a Walkman and today everyone has an iPod.)

Of more concern than a failure to appreciate these historical facts are the continued misstatements, particularly concerning patent law, that once again grace the pages of the Times. Quoting Daniel S. Greenberg, another anti-patent pundit, the article asserts that, had the current patent regime existed when Watson and Crick discovered the double helical structure of DNA, they would have tried to patent it. Like the hyperbole of others (see "Science Fiction in The New York Times"), the statement is not only wrong it is demonstrably wrong: the double helix, like the relationship between mass and gravity or the fact that water boils at 100°C (at sea level) is an unpatentable phenomenon of nature.

Indeed, Mr. Greenberg proves the converse of one of the arguments inherently advanced by the article: that somehow "corporate secrecy" has besmirched the heretofore pure pursuit of knowledge. Prior to the errant speculation that Watson and Crick would have patented the double helix, the article ascribes to him this apocryphal description of how science was done in 1950’s England:

When James Watson and Francis Crick were homing in on DNA’s double-helix structure in the 1950s, they zealously guarded their work from prying eyes until they could publish their findings, to be certain that they would get the credit for making the discovery.

Similar descriptions have come from Jim Watson himself, in The Double Helix and elsewhere. Thus, it seems that a due concern for advancing one’s own career provided ample motivation for jealously guarding research results very much before the advent of university patenting under Bayh-Dole.

Similarly wrong are the purported consequences of the infiltration of filthy lucre into the ivory towers of academe. The piece bemoans that "[b]lue sky" research — the kind of basic experimentation that leads to a greater understanding of how the world works — has largely been set aside in favor of projects considered to have more immediate market potential." Perhaps a quick perusal of the grant proposals to the National Institutes of Health or the National Science Foundation would have helped, since these are replete, even today, with exactly this kind of "blue sky" research. The reason is simple, and well understood by those who actually do the science: technology is when you know the answer, and the important and exciting work in science comes when you not only don’t know the answer, you aren’t really sure about the question. Grant proposals, while needing to convince the funding agency that the proposal has a chance of providing useful information, are not geared towards technological applications; perhaps Ms. Rae-Dupree is confusing this type of grant with applications for Small Business Innovation Research (SBIR) grants, which resemble the types of non-"blue sky" research she mentions.

Also untrue is that "[p]atenting a new basic science technique, or platform technology, puts it out of the reach of graduate students who might have made tremendous progress using it." Patents are meant to prevent commercial activity, and although there is no "pure research" exemption in patent law, there is a higher law in play: never sue anyone who doesn’t have any money. It is extremely unlikely that a graduate student, working on a dissertation that is used merely to fulfill the requirements of a degree and perhaps publish a paper in a scientific journal, would ever have need to worry about being sued for patent infringement. The proof of this state of affairs is that the poster child for the supposed risk of patent infringement, Madey v. Duke University, has never been used to support an infringement action for non-commercial research activities.

Many of the critics cited in the article represent industry, and they recite how the current state of affairs — where universities can patent their inventions — has stymied commercial application of these inventions. This is undoubtedly the case; it is always easier just to take the fruits of another’s labor than to pay for them. Uncritical reproductions of these types of complaints from industry can serve only one purpose, to persuade policymakers to rethink the Bayh-Dole scheme. While this might be good for those industries who have recently shown disdain for any innovation other than their own, it would not be good for the rest of us.

There are certainly some inefficiencies in the current system that are mentioned in the article, for example that only a few major universities have reaped the greatest benefits of licensing patented technology. Rather than damning the effort, however, this data merely confirms that invention, and profitable commercial exploitation of invention, is unpredictable, serendipitous and a lot harder than most of us (including, perhaps, some tech transfer managers) contemplate. The fact is that permitting university patenting over the past quarter century has fostered wide innovation, new products including new drugs and therapies, and promoted U.S. jobs and the economy. We would be foolish indeed to go back to having U.S. academia let corporations free-ride on the innovations produced as the fruits of their research.

For additional information regarding this and other related topics, please see:

• "New York Times to Innovation: Drop Dead," April 30, 2008
• "The Continuing Assault on Innovation at The New York Times," July 15, 2007
• "The Anti-Patent Beat Goes on at The New York Times," July 1, 2007
• "Science Fiction in The New York Times," February 13, 2007
• "Anti-Patent ("Sullivan?") Malice by The New York Times," January 29, 2007
Conference & CLE Calendar

September 7, 2008

September 11, 2008 – Developments in Pharmaceutical and Biotech Patent Law (Practising Law Institute) – New York, NY

September 11-12, 2008 – Current Issues in Complex IP Licensing (Law Seminars International) – Philadelphia, PA

September 15-16, 2008 – Biotech Patents*** (American Conference Institute)

September 16, 2008 – The Legacy of Judge Howard T. Markey*** (The Center for Intellectual Property Law, John Marshall Law School) – Chicago, IL

September 21-23, 2008 – 2008 Annual Meeting (Intellectual Property Owners Association) – San Diego, CA

September 22-23, 2008 – FDA Boot Camp*** (American Conference Institute)

September 22-23, 2008 – Patent Litigation 2008 (Practising Law Institute) – San Francisco, CA

September 22-23, 2008 – 2008 World Stem Cell Summit (Genetics Policy Institute) – Madison, WI

September 23-24, 2008 – Biotech Patenting (C5) – London, England

October 6-7, 2008 – Patent Litigation 2008 (Practising Law Institute) – McLean, VA

October 7-8, 2008 – Global Patent Litigation*** (American Conference Institute) – New York, NY

October 15, 2008 – Developments in Pharmaceutical and Biotech Patent Law (Practising Law Institute) – San Francisco, CA

October 15-16, 2008 – Pharmaceutical Congress on Paragraph IV Disputes*** (Center for Business Intelligence) – Philadelphia, PA

October 15-16, 2008 – Advanced Courses (Patent Resources Group) – Santa Ana Pueblo, NM

October 15-17, 2008 – Maximizing Pharmaceutical Patent Lifecycles*** (American Conference Institute) – New York, NY

October 23-24, 2008 – Patent Litigation 2008 (Practising Law Institute) – Chicago, IL

October 28-29, 2008 – Pharma/Biotech IP Due Diligence*** (C5) – Amsterdam, Netherlands

November 10-11, 2008 – Patent Litigation 2008 (Practising Law Institute) – Atlanta, GA

November 12-14, 2008 – Structuring, Negotiating and Managing Pharma/Biotech Collaborative Agreements (American Conference Institute) – New York, NY

November 17-18, 2008 – Pharmaceutical and Biotech Patent Opinion Writing*** (American Conference Institute) – Boston, MA

November 17-18, 2008 – Patent Litigation 2008 (Practising Law Institute) – New York, NY

November 19-20, 2008 – Paragraph IV on Trial*** (American Conference Institute) – New York, NY

December 8-9, 2008 – Pharmaceutical and Biotech Patent Opinion Writing*** (American Conference Institute) – Atlanta, GA

January 12-13, 2009 – Pharmaceutical and Biotech Patent Opinion Writing*** (American Conference Institute) – San Diego, CA

***Patent Docs is a media partner of this conference or CLE
ACI Pharmaceutical and Biotech Patent Opinion Writing Conference

September 5, 2008

American Conference Institute (ACI) will be holding its Pharmaceutical and Biotech Patent Opinion Writing conference on November 17-18, 2008 in Boston, MA. The conference, which will be repeated on December 8-9, 2008 in Atlanta, GA and on January 12-13, 2009 in San Diego, CA, will provide hands-on training with respect to:

• Writing non-infringement and validity opinions;
• Gauging the application of safe harbor;
• Incorporating In re Seagate into your analysis; and
• Clarifying the meaning, impact, and limits of the patent opinion.

In particular, ACI’s faculty will offer presentations on the following topics:

• Clarifying the evolving impact of In re Seagate;
• Criteria for determining whether you need a patent opinion;
• Establishing the type of patent opinion needed by the client and the reason for the patent opinion;
• What to put in writing, what to leave out;
• Measuring the scope of the patent opinion;
• Determining the level of certainty in the patent opinion;
• Defining the elements of an effective FTO search;
• Doctrine of equivalents;
• Effectively searching prior art;
• Writing the non-infringement patent opinion;
• Writing the validity opinion; and
• Minimizing access to the patent opinion.

The agenda for the Pharmaceutical and Biotech Patent Opinion Writing conference can be found here. A complete brochure for this conference, including an agenda, list of speakers, and registration form can be downloaded here.

The registration fee for this conference is $1,695. Those interested in registering for the conference can do so here, by calling 1-888-224-2480, or by faxing a registration form to 1-877-927-1563.

Patent Docs is a media partner of the Pharmaceutical and Biotech Patent Opinion Writing conference.
John Marshall Law School to Host Conference Celebrating Legacy of Judge Markey

September 5, 2008

The Center for Intellectual Property Law at the John Marshall Law School in Chicago, IL will be presenting a one-day conference entitled: "The Legacy of Judge Howard T. Markey" on September 16, 2008. The conference will celebrate the legacy of Judge Markey, who served on the bench from 1972 to 1991, played a historic role in the founding and initial administration of the Federal Circuit, and was the first judge to sit with every one of the thirteen circuit courts of appeal across the nation. The conference will consist of four panel discussions and include a luncheon keynote address from Justice Antonin Scalia of the U.S. Supreme Court. The four panel discussions will address the following topics:

• Judge Markey’s Legacy in Patent Law: Patent Prosecution and Patent Scope
• Judge Markey’s Legacy in Patent Law: Patent Licensing, Infringement, and Enforcement
• Judge Markey’s Legacy in the Founding and Administration of the Federal Circuit Court
• Judge Markey’s Legacy in Legal Education and the American Inns of Court

The registration fee for the conference ranges from $95 (government, judicial, or academic registration) to $195 (general registration). Those interested in registering for the conference must do so by completing and submitting a registration form. A complete brochure for the conference, including an agenda, list of speakers, and registration form can be downloaded here.

Patent Docs is a sponsor of the conference.
Isis Pharmaceuticals Adds to Crooke RNAi Patent Estate

September 4, 2008

By Donald Zuhn —

Isis Pharmaceuticals, Inc. announced today that the U.S. Patent and Trademark Office has issued notices of allowance for U.S. Application Nos. 10/281,312 and 10/281,297. According to the company’s press release, the two allowances "significantly expand" the scope of Isis’ Crooke patent estate — a family of patents based on the research of Dr. Stanley Crooke and others at Isis to identify and design RNA molecules that harness cellular RNase enzymes as antisense drugs, including RNAi and microRNA therapeutics. Isis noted that the two allowed applications are directed to methods of treating patients by administering an siRNA or a single-stranded RNA-containing compound and to pharmaceutical compositions containing single-stranded RNA-like compounds.

The Crooke patent estate, which includes U.S. Patent Nos. 5,898,031 and 6,107,094, is licensed by Isis Pharmaceuticals to Alnylam Pharmaceuticals, Inc. for the development of double-stranded RNAi therapeutics and to Regulus Therapeutics LLC, a joint venture between Isis and Alnylam, for the development of microRNA-based therapeutics. Discussing the allowances, Dr. Crooke, Isis’ Chairman and CEO, observed that the company’s patent position with respect to RNA-based therapeutics was "unparalleled" and added that "[t]he Crooke patent series provides broad protection against competitors who are developing RNA-based drugs, including siRNAs." Alnylam CEO Dr. John Maraganore noted that the allowances were "particularly important because they broaden the scope of our IP covering pharmaceutical compositions and methods of treating patients with RNAi therapeutics." Regulus CEO Dr. Kleanthis Xanthopoulos similarly noted that "[t]hese new patent allowances significantly strengthen our
efforts to advance microRNA therapeutic products to patients."

With respect to the ‘312 application, representative allowed claim 89 recites:

89. A method of treating a patient having a disease characterized by the undesired production of a protein encoded by a target RNA, comprising administering to said patient a pharmaceutically effective amount of an oligomeIic compound, wherein said compound:
(i) is specifically hybridizable with said target RNA;
(ii) is 15 to 25 nucleoside subunits in length;
(iii) comprises a plurality of nucleoside subunits with 2′ -hydroxyl pentofuranosyl sugar moieties; and
(iv) compIises at least one modified nucleoside subunit, wherein said modification increases affinity of said compound to said target RNA or increases resistance of said compound to single-stranded nucleases.

With respect to the ‘297 application, representative allowed claims 94 and 111 recite:

94. A composition comprising a pharmaceutically acceptable diluent or carrier and a single-stranded oligomeric compound, wherein said compound:
is 15 to 25 nucleoside subunits in length;
specifically hybridizes with a preselected target RNA;
comprises at least four consecutive nucleosides with 2′ -hydroxyl-pentofuranosyl sugar moieties; and
further comprises at least one sugar modified nucleoside subunit, wherein the modification improves affinity or specificity of said compound to said target RNA or increases resistance of said compound to single-stranded nucleases.

111. A composition comprising a pharmaceutically acceptable diluent or carrier and a single-stranded oligomeric compound, wherein said compound:
is 15 to 25 nucleoside subunits in length;
is specifically hybridizable with a preselected target RNA;
comprises at least one sugar modification; and
comprises a plurality of nucleoside subunits with 2′-hydroxyl pentofuranosyl sugar moieties.
BIO Discusses Legislative Accomplishments

September 3, 2008

By Kevin E. Noonan —

Earlier today, Patent Docs participated in a conference call with Jim Greenwood, the President and CEO of the Biotechnology Industry Organization (BIO) and Joshua Boger, Ph.D., Chairman of BIO’s Board and President and CEO of Vertex Pharmaceuticals Inc. Mr. Greenwood, who represented Pennsylvania’s Eighth District in the U.S. House of Representatives from January 1993 through January 2005 prior to his BIO appointment, had invited the press as well as biotech and pharma bloggers to participate, where he and Dr. Boger provided a briefing on BIO’s accomplishments during the 110th Congress and its expectations and hopes for the new Congress and the next administration.

Mr. Greenwood (at left) started the briefing by recounting BIO’s legislative successes. He mentioned the challenges BIO faced with the change in the majority party in Congress, mentioning that the new Congress had new perspectives and priorities. Despite these challenges, he declared 2008 "a good year" for BIO and its member companies. Among the victories, some were ones of avoidance, such as there being no "bad" follow-on biologics legislation passed. There were several bills introduced in this session of Congress that BIO opposed; the latest bill, which Mr. Greenwood reported now has 40 co-sponsors in the House, is one that BIO supports, and Mr. Greenwood predicted that it would be introduced early in the next Congress. Mr. Greenwood was also gratified by the recent report from the Government Accounting Office (GAO) that confirmed BIO estimates that the amount to be saved under Senator Kennedy’s follow-on biologics bill would be less than its advocates predicted.

Mr. Greenwood also counted among BIO’s successes failure to pass patent "reform" legislation; during the question and answer session he expanded on this point, saying that the conventional wisdom that the fight over the patent bill was between the biotech/pharma industry and the IT industry was not entirely accurate. He credited BIO’s efforts to engage universities, sole inventors, and small, entrepreneurial start-ups as important in convincing the Senate that the bill did not represent the kind of reform the patent system may need.

BIO is also supporting increased funding for the Food and Drug Administration, and Mr. Greenwood called this one of BIO’s top priorities for the new Congress. He mentioned various funding and budgetary efforts to increase appropriations for FDA, as well as mentioning the importance for the new administration and Congress to make naming an FDA head one of its top priorities. Other successes mentioned by Mr. Greenwood include tax credits for cellulosic and renewable fuels research and development, preventing passage of new Medicaid rebate increases, passage of the Genetic Information Nondisclosure Act (GINA), and he gave new efforts to increase funding of the Small Business Innovation Research program "a 50:50 chance" of being approved.

Turning to the future, Mr. Greenwood said that, no matter which candidate won the Presidency there would be some form of health care reform enacted, and said that BIO was committed to supporting reform that would be comprehensive and support innovation. BIO is also using its contacts with the presidential campaigns to impress upon the candidates the urgency in having a new FDA administrator appointed and approved by the Senate as early in the new administration as possible.

Both men expanded on this theme during the question and answer period; Dr. Boger (at right) raising the paradox that the monies spent on the human genome project had resulted in an unprecedented amount of new information leading to new therapies over the past 10 years, but that the American public was not seeing the benefit of many of these breakthroughs due to flat funding of FDA. He said that it was time for the FDA to cease being a political punching bag in this regard. Mr. Greenwood mentioned that while the PFUDA system had increased drug company ("user fee") funding of FDA from 7% to >60% of the agency’s budget, user fees also created the false impression that industry was too influential in the drug approval process. He said it would be better if user fees accounted for about 50% of agency funding, which would require an additional $200 million in taxpayer funding over 5 years, an initiative BIO supports. He also mentioned that FDA needed more funds to support inspections of API and generic drug suppliers overseas, in view of the heparin incident earlier this year, and that BIO supports passage of a drug import safety bill (although in view of the different industry sectors involved, he acknowledged that this will need thorough vetting by Congress).

Turning to the election, Mr. Greenwood said that both candidates have "said good things" about biotechnology, and both support expanded Federal government support for embryonic stem cell research; in this regard, Mr. Greenwood predicted that we would return to science-based, rather than ideologically-based, policymaking on stem cell research. He noted that the candidates differed in the details, mentioning that Senator Obama was supportive of increasing investment in biotech research and the FDA, as well as expansion of the H-1 visa program. He noted, however, that both candidates have also been critical of the biotech/pharma industry, and have supported policies (such as drug re-importation and government involvement in Medicare Part D price negotiations) that BIO opposes.

Dr. Boger said that the election represented an "enormous opportunity" for BIO and its member companies to participate in a new dialog on these issues, one that is focused on problem-solving rather than partisan finger-pointing. He said that decreasing health care costs was easy: cure more disease, something that is BIO’s companies’ business. Mr. Greenwood said BIO was engaging the campaigns in this dialog, meeting with campaign staffers, and initiating studies to provide the data that supports BIO’s positions. This is part of a broad-based communication plan to educate policymakers as well as the public about the importance of biotechnology in health care reform and the availability of better health care in this country.

During the question-and answer period, Mr. Greenwood commented generally on the patent reform bill authored by Senator Kyl of Arizona; while admitting that he hasn’t studied the bill (his staff has), he said the BIO supports many of the provisions in the bill and that BIO will participate in the debate in the next Congressional session. The goal, he said, is not to have one industry disadvantaged at the expense of others, and that BIO’s alliances with universities, small inventors, and start-up biotech companies will help make the case in the next Congress.

Despite believing that both candidates have supported expanded Federal funding research for embryonic stem cell research, in response to a question, Mr. Greenwood did concede that Senator McCain may be refining his position on the subject (presumably due to pressure from the conservative Republican base). Mr. Greenwood mentioned that the embryonic stem cell bill vetoed in the last session by President Bush was H.R. 3, and predicted that a similar bill would have the same priority of being one of the first bills introduced in the next Congressional session. BIO will support passage of an embryonic stem cell bill and believes that it would be "surprising" if Mr. McCain vetoes it should he be elected President. He also said that the new President could change Federal policy as President Bush had done, by executive fiat, but that BIO preferred that Congress set policy, because that would permit the political process to work.

Mr. Greenwood addressed a question regarding the candidates’ criticism of biotech drugs as being a source of rising health care costs. He said he expected that a follow-on biologics bill would change the present "non-competitive" environment for these drugs, and that BIO is committed to getting a "good bill" passed that addressed questions of access and indemnification for high drug costs. He also said that there was not sufficient time in this session to have a realistic chance of passing a bill before next year. Dr. Boger maintained that breakthrough biotechnology drugs were actually a bargain, when development costs and the morbidity and mortality costs of not having these drugs were factored into the analysis.

On other policy matters, Mr. Greenwood affirmed that BIO would be filing an amicus brief with the Federal Circuit in the Tafas v. Dudas case, and that BIO would not be endorsing either presidential candidate, saying that there were not sufficient differences between the candidates on issues important to BIO’s member companies. He did acknowledge that BIO’s campaign contributions are more evenly distributed between Democratic and Republican candidates than they have been in the recent past (with Senator Obama receiving slightly more campaign contributions than Senator McCain).

One area where Mr. Greenwood and Dr. Boger expanded on the prepared remarks during the question and answer period was the issue of comparative effectiveness of drugs. Dr. Boger said Congress should "let doctors be doctors" and make the individual medical decisions in each patient’s best interest, and that the fact that a particular formulation or species of API is effective in 80% of the population should not impair a doctor’s ability to prescribe (or a patient’s ability to obtain reimbursement) for a different drug that works for them. Comparative effectiveness cannot be used for producing drug formularies, he said. Mr. Greenwood added that the diversity of patient reactions as having a big effect, and said that legislation and/or regulations were needed that prevented payors from reimbursing alternative drugs.

A podcast of the briefing can be obtained here.

For additional information on this and other related topics, please see

• "BIO CEO Provides Update on Patent Reform and Follow-on Biologics Legislation – Part II," February 14, 2008
• "BIO CEO Provides Update on Patent Reform and Follow-on Biologics Legislation – Part I," February 14, 2008
• "BIO CEO Provides Briefing on Follow-On Biologics and Patent Reform," September 18, 2007
USPTO News: USPTO and UKIPO Extend Patent Prosecution Highway Pilot Program

September 3, 2008

By Donald Zuhn —

Last week, the U.S. Patent and Trademark Office announced that the Patent Prosecution Highway (PPH) pilot program with the United Kingdom Intellectual Property Office (UKIPO), which was initiated on September 4, 2007, would be extended until further notice. The USPTO and UKIPO will continue to periodically monitor the program to determine whether it should be fully implemented at a later date.

Under the extension, the USPTO and UKIPO will continue to accept applications for participation in the PPH, which permits an applicant having an application whose claims have been allowed by one office to fast track the examination of an application in the other office, such that the latter application would be examined out of turn. In particular, an applicant receiving a ruling from either the UKIPO or the USPTO that at least one claim in an application is patentable may request that the other office fast track the examination of corresponding claims in the corresponding application.

The USPTO also announced that under modifications to the PPH pilot program introduced last January, certain applications based on PCT filings are now eligible for participation in the PPH program.

For additional information on this and other related topics, please see:

• "Patent Prosecution Highway Extended to IP Australia," April 2, 2008
• "Patent Prosecution Highway Network Expands to Canada & Korea," January 29, 2008
• "USPTO Announces Two Additional Partners in the Patent Prosecution Highway Pilot Program," January 17, 2008
• "USPTO and JPO to Implement Patent Prosecution Highway on Full-Time Basis," December 27, 2007
• "USPTO and UK IPO to Collaborate on Patent Prosecution Highway," September 14, 2007
• "Patent Prosecution Highway Pilot Program to Be Extended," June 28, 2007

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