By Christopher P. Singer —

The U.S. Patent and Trademark Office sent out an e-Commerce update on June 26, 2008 that provided information regarding the release of enhancements to Private PAIR and Public PAIR, the indexing of request documents for the Patent Prosecution Highway (PPH), and access to design patent applications using the Priority Document Exchange (PDX).

Private and Public PAIR Enhancements

The USPTO plans to release Private PAIR 7.3/7.4 and Public PAIR 3.1 on July 4, 2008.  The enhancements include several updates such as e-Office Action Pilot Program improvements to the e-mail notifications, which will now list the IFW document code and mailroom date, in addition to the application number and Attorney Docket Number.  This, of course, is only meaningful to participants in the e-Office Action Pilot Program.  You can register for the e-Office Action Pilot Program by e-mailing your request to participate and Customer Numbers to the PAIR team at ebc@uspto.gov.  Improvements are also being made to National Stage Entry Application and Status Data, PAIR Text Messages that will notify users regarding urgent messages, and a new PAIR Announcement Tab for easy reviewing of recent PAIR-related announcements.  More information relating to the PAIR enhancements can be found here.

Indexing Patent Prosecution Highway Request Documents

When submitting a Patent Prosecution Highway (PPH) Request, all documents should be indexed as "Petition to Make Special under Patent Pros Hwy," with the exceptions of preliminary amendments and information disclosure statements (IDSs), which should be indexed as usual.  More information about PPH can be found here.

Priority Document Exchange (PDX)

The Priority Document Exchange (PDX) program does not include design patent applications.  Japanese and European design applications are located in electronic systems separate from the utility applications, which are not accessible via PDX.

The EBC Customer Service Center is also available to answer your specific questions about EFS-Web, PAIR, PKI, or any other aspect of the e-Commerce initiative.  You can contact the EBC by phone at 866-217-9197 (toll-free) or 571-272-4100 or by an e-mail at: ebc@uspto.gov.

    By Kevin E. Noonan —

As reported by Patent Docs earlier this week, the U.S. Patent and Trademark Office took the podium at BIO 2008 last week in San Diego, in the person of Dr. George Elliott, a Director in Group 1600.  Like his boss, John Doll, Director Elliott is a personable and friendly PTO presence as a speaker, and he did a good job of explaining Patent Office initiatives like worksharing programs and how the Group is applying the KSR Int’l Co. v. Teleflex Inc. decision.  It was when he turned to his last topic, the "new" written description training materials (to be used by examiners in implementing the "old" written description guidelines promulgated in 2001) that his talk reminded us that we were listening to a PTO official from the Dudas administration.

Specifically in this regard, Dr. Elliott spoke about Example 11, dealing with how the written description requirement would be applied by the Office for claims reciting a polynucleotide or polypeptide sequence that shares percent identity with another sequence (see "An Analysis of the New Written Description Training Materials – DNA Hybridization & Percent Identity").  We (and others) noted a curious aspect of the "new" way the Office would apply the requirement.  In the past, it was commonplace to recite claims having the following structure:

Claim 2:  An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2; wherein the polypeptide has activity X.

The limitation that the claimed sequences encompassed only functional species (polypeptides having activity X) was intended to exclude inoperative species.  Curiously, the new training materials instructed examiners to reject such claims unless the specification contained (or the art recognized) a structure-function relationship between the sequence and "activity X."  In explicating the Example, the training materials assert that where the specification discloses a single polypeptide sequence (or the putative sequence deduced from a cloned sequence), and without any disclosure regarding which amino acid residues could be altered whist retaining the recited activity, claims like the one above would fail to satisfy the written description requirement.

The following claim, on the other hand, would pass muster under the new application of the written description requirement:

Claim 1:  An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2.

The training materials justify this distinction because "[w]ith the aid of a computer, one of skill in the art could have identified all of the nucleic acids that encode a polypeptide with at least 85% sequence identity with SEQ ID NO: 2."

The more astute student of the present regime questioned whether there would be any other consequences for claims presented that did not recite any activity for the claimed polypeptide, and hence encompassed both operative and inoperative species.  And Dr. Elliott provided the answer:  while claim 1 satisfied the written description requirement, such a claim would fail to satisfy the enablement requirement.  When questioned after his formal presentation, Dr. Elliott further explained that the Office considers this equitable because the overwhelming majority of altered polypeptides would be inoperative, and it has long been the law that a claim encompassing an overwhelming number of inoperative species constitutes undue experimentation to be practiced by the public (once a patent’s term has expired).

None of this, of course, is set out in the training materials (save the following "Practice Note" set forth at the end of the Example):

This, of course, is the tip-off, but it is more in the tradition of patent law being comprised of "traps for the unwary" than an administration trying to come to an equitable balance between claim scope and sufficiency of disclosure.  And while the Example cites some standard protein structure references, the Office is mistaken in the view expressed by Director Elliott about the consequences of amino acid sequence variation on protein activity.  Biologists have recognized for over forty years that most variation in most proteins is neutral, even when it has structural consequences like altering mobility on starch gels or changing a protein’s pI.  Proteins, in short, are not so fragile, and that is consistent with the type of genetic variation needed to drive and sustain evolution.  More recently, the amount of genetic variation in an individual was found to be much higher than previously recognized, mostly due to insertions, deletions, and rearrangements in chromosomal DNA inherited from both parents (see "A Complete Diploid Human Genome Reveals Some Surprises").  The Office seems to believe that the fact that it is (typically) impossible to predict whether a particular change in a particular position will affect protein structure is enough to support a requirement that 35 U.S.C. § 112, first paragraph, requires explication of the effects of every change at every position.  This thinking is illustrated in a recent Board decision, In re Porro, which will be the subject of a future post but is enough to disturb the sleep patterns of any conscientious biotech patent practitioner (or applicant).

For now going forward, the most prudent course may be to disclose species orthologs or allelic variation (when known), to identify both invariant residues and residues that have been changed by nature.  Sequence alignments, or inclusion of "consensus" amino acid sequences in a Sequence Listing, should also be useful in addressing enablement rejections arising from presenting claims that satisfy the written description requirement as now applied.  And the Federal Circuit may yet resolve the issue, since one of the rejections appealed in Ex parte Kubin was for failure to satisfy the written description requirement in a claim reciting 80% amino acid sequence identity (and the Office’s interpretation appears to violate the standard set forth by the Court in Enzo Biochem, Inc. v. Gen-Probe Inc.; see "Briefs for In re Kubin filed by Amgen and BIO").  Until this issue gets resolved, however, biotech patent applicants and their counsel can include the latest Patent Office "gotcha" game to the list of difficulties they can expect to encounter when trying to protect their inventions.

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

• "Docs at BIO: Panel Discusses Impact of USPTO Rules Changes and Patent Reform Legislation on Biotech Patenting," June 23, 2008
• "Docs at BIO: Representatives from JPO, EPO, SIPO, and USPTO Discuss Recent Developments in Japan, Europe, China, and the U.S.," June 22, 2008
• "Docs at BIO: Steve Burrill’s State of the Biotechnology Industry Report 2008," June 19, 2008

    By Christopher P. Singer —

In April, the U.S. Patent and Trademark Office announced
that it had updated the training materials to be used by examiners in
the examination of patent applications for compliance with the written
description requirement of 35 U.S.C. § 112, first paragraph.  The revised training materials supersede and replace the previous set of training materials
issued by the Patent Office in 1999.  The new training materials
provide seventeen examples, of which fourteen are specifically related
to biotech inventions.  In particular, the biotech-specific examples
address expressed sequence tags (ESTs) (example 4), a partial protein
structure (example 5), DNA hybridization (example 6), allelic variants
(example 7), bioinformatics (example 8), protein variants (example 9),
a product claimed by its function (example 10), a polynucleotide or
polypeptide sequence sharing percent identity with another sequence
(example 11), antisense oligonucleotides (example 12), antibodies to a
single protein (example 13), antibodies to a genus of proteins (example
14), a genus with widely varying species (example 15), a process claim
where novelty resides in the process steps (example 16), and methods of
using compounds claimed by functional limitations, methods of
identifying compounds, and compounds identified by such methods
(example 17). Continuing our review, Patent Docs provides an overview of the example covering aspects of protein variants.

Example 9 – Protein Variants

Example 9 contains two claims directed to an isolated protein of a particular sequence (SEQ ID NO: 3) or a variant thereof.  This Example is essentially unchanged from the variant example in the former written description guidelines (presented therein as Example 13).  The exemplary claims recite:

Claim 1:  An isolated protein comprising the amino acid sequence shown in SEQ ID NO: 3.

Claim 2:  An isolated variant of the protein of claim 1.

The hypothetical specification discloses that applicant had isolated from liver a 65 kDa protein that has tumor necrosis activity.  The specification also provides the protein sequence (SEQ ID NO: 3).  The specification states that the invention provides protein variants of SEQ ID NO: 3 having one or more amino acid substitutions, deletions, insertions, and/or additions, and that making such protein variants is routine in the art.  However, the specification fails to include any further description of the claimed variants and also fails to define when a sequence is no longer a variant of SEQ ID NO: 3.

Not surprisingly, claim 1 is adequately supported by the written description because the specification provides SEQ ID NO: 3, the structure of which is present within the entire genus of proteins encompassed by the claims (e.g., fusion proteins comprising SEQ ID NO: 3).  Those skilled in the art, given the disclosure in the specification and general knowledge in the art, would recognize that the applicant was in possession of the invention recited in claim 1.

The fate of claim 2 is not as rosy.  The Office’s analysis goes to great lengths to discuss the many shortcomings of the hypothetical disclosure and concludes that claim 2 lacks adequate written description.  The analysis concedes that pre-existing knowledge in the art adequately supplements the description as far as addition variants are concerned (e.g., fusion proteins as supported for claim 1).  Regarding the inadequacy of the disclosure, the Office notes that the disclosure (1) places no limit on the number of amino acid substitutions, deletions, insertions and/or additions; (2) fails to describe the complete structure of any members of the genus encompassed by claim 2; (3) fails to describe the physical or chemical characteristics for any substitution, deletion, or insertion variants; (4) fails to disclose any correlation between the structure of the variants and the disclosed SEQ ID NO: 3; and (5) fails to correlate structure with function of any variant.  Consequently, the Office states that the specification fails to satisfy the written description requirement for Claim 2.

It is particularly difficult to derive anything useful from this example.  Beyond the conclusion that fusion proteins are well known in the art and are supported with minimal disclosure, the Office provides no guidance for an application that contains any amount of significant disclosure regarding variants.  This example in particular seems to suggest that written description can be satisfied only for that which is explicitly disclosed and exemplified in the specification.

For additional information on this topic, please see:

• "Antisense," May 13, 2008
• "Antibodies to a Single Protein & Antibodies to a Genus of Proteins," May 12, 2008
• "ESTs & Partial Protein Structures," May 8, 2008
• "DNA Hybridization & Percent Identity," May 6, 2008

    By Donald Zuhn —

Last Thursday, a diverse panel comprising both in-house and outside counsel and both corporate and venture capital interests participated in a breakout session at the BIO International Convention to discuss IP challenges and strategies for biotech and pharma companies as a result of pending USPTO rules changes and possible patent reform legislation.  Participating in the panel were Dr. Jeffrey W. Guise, a Partner with Wilson Sonsini Goodrich & Rosati; Ms. Esther Kepplinger, the Director of Patent Operations for Wilson Sonsini Goodrich & Rosati; Dr. Kim Kamdar, a Principle with Domain Associates; Dr. Daniel P. Gold, the founder and former Chief Scientific Officer of Favrille, Inc.; and Ms. Hazel Aker, Senior Vice President, General Counsel, and Secretary of Cadence Pharmaceuticals, Inc.

In the first half of the session, Ms. Kepplinger provided an overview of pending USPTO rules changes and an update regarding patent reform.  Following Ms. Kepplinger’s presentation, Dr. Guise moderated a panel discussion to determine how venture capitalists (represented by Dr. Kamdar), corporate executives (represented by Dr. Gold), and in-house counsel (represented by Ms. Aker) thought the rules changes and patent reform would impact biotech and pharma patenting.

With the claims and continuations rules being permanently enjoined, the IDS rules being seemingly put on hold (perhaps as a result of the Patent Office’s questionable economic impact analysis), the alternative claiming rules being re-published for comment (again, as a result of the Patent Office’s questionable economic impact analysis), and patent reform legislation being removed from the Senate calendar, one would have thought that Ms. Kepplinger might have very little to say regarding the topic of rules changes and patent reform.  However, the former Deputy Commissioner for Patent Operations at the USPTO came armed with a number of interesting statistics and valuable insight gleaned from her work in the Patent Office.

Ms. Kepplinger (at left) began by asserting that the collection of rules packages proposed by the USPTO in the past year would neither reduce the application backlog nor improve patent quality.  She also contended that the Patent Office had not done much internal review to determine whether, and how, the Office had contributed to the backlog.  If the Office had done so, Ms. Kepplinger argued that it would have found that many of its actions actually contributed to the backlog.

According to Ms. Kepplinger, the ill-fated continuation and claims rules serve as a perfect example of the Patent Office’s flawed logic, which blamed the backlog on applicants’ filing of increasing numbers of continuation applications.  Citing a study conducted at the George Mason University School of Law (see "Improving Patent Examination Efficiency and Quality: An Operations Research Analysis of the USPTO, Using Queuing Theory"), Ms. Kepplinger noted that contrary to the Office’s hypothesis, the backlog has been caused by the issuance of too many non-final Office actions.  In particular, the George Mason study found that divisional and continuation filings have remained fairly stable over the past seven years, while RCEs have increased from 8.3% to 19.6% of total filings.  Ms. Kepplinger argued that this actually indicates that some examiners have been "gaming the count system."

Ms. Kepplinger next discussed statistics related to actions per disposal (APD; the number of actions issued before an application is allowed or abandoned).  Reflecting on her five years as Deputy Commissioner, she noted that the Office had always achieved an APD of about 2.3, and that between 1985 and 2004, the APD had remained at this level.  However, as shown below, the APD steadily rose between 2004 and 2007:

2004: 2.27
2005: 2.60
2006: 2.76
2007: 2.85

Ms. Kepplinger argued that while the jump in APD may seem small, it actually accounts for an increase of more than half an action per application.  Even more interesting was Ms. Kepplinger’s observation that the USPTO had made the above figures available only after a FOIA request had been filed.  Moreover, Ms. Keplinger noted that the USPTO had recently begun to include design applications in its APD calculations (something she stated was not done during her tenure with the Office), which would skew the numbers in favor of the USPTO’s position (i.e., yielding current APD values that are closer to past APD values).

Turning her focus to allowance rates, Ms. Kepplinger presented a graph (originally presented by Director Dudas) that clearly indicated that allowance rates had remained fairly constant between 1975 and 2000 (ranging from 60% to just over 70%), and had dropped significantly since 2000.  Ms. Kepplinger primarily blamed increased RCE filings for the drop in allowance rate (noting that when RCEs are subtracted from the post-2000 totals, the allowance rate returns to pre-2000 levels).  According to Ms. Kepplinger, other causes for the drop in allowance rate include:

1.  The USPTO’s goal to achieve a 3.5% error rate (Ms. Kepplinger noted that supervisor bonuses are keyed to this goal, and that the USPTO recently began including design applications in its error calculations – presumably to keep the rate at or below 3.5%);
2.  The USPTO’s desire to have a "second set of eyes" review applications prior to allowance;
3.  Massive hiring of new (and inexperienced) examiners;
4.  The reluctance of examiners to allow applications (Ms. Kepplinger noted that "you can’t make a mistake if you don’t allow"); and
5.  The KSR Int’l Co. v. Teleflex Inc. decision.

The latter part of Ms. Kepplinger’s presentation was devoted to a discussion of the status of various USPTO rules packages and patent reform legislation.  With respect to the alternative claiming rules (which were recently re-published for comment; see "Patent Office Publishes Notice Regarding Impact of Proposed Markush Claims Rules on Small Entities"), Ms. Kepplinger provided four suggestions for dealing with these rules once they are promulgated (as she expected they would be):

1.  Use true generic claims, since the alternative claims rules will not apply to such claims (e.g., a claim reciting a citrus fruit will fall outside the rules, while a claim reciting an orange, grapefruit, or lemon would be encompassed by the rules);
2.  If possible, identify one embodiment that falls within two restricted groups, since such an embodiment could be used to argue that restriction was improper (Ms. Kepplinger noted that petitions on restriction in Group 1600 are granted about 60% of the time);
3.  Interview the case; and
4.  Be prepared to appeal.

Moving to the IDS rules, Ms. Kepplinger offered the following suggestions for dealing with these rules:

1.  Review the references to be cited and try to remove cumulative references from the list;
2.  Memorialize your analysis of references and place it in the file; and
3.  Utilize alternative methods of disclosing references (e.g., present references at an Interview).

On the subject of the continuation and claims rules, Ms. Kepplinger stated that "it’s not clear that these will be gone forever," observing that one possible outcome of the USPTO’s loss in Tafas/GSK v. Dudas is that the Office will try that much harder to get Congress to grant it substantive rulemaking authority.  On the bright side, Ms. Kepplinger argued that Tafas/GSK "has created a roadmap to challenge other rules packages."  Finally, in addressing the stalled patent reform bill in the Senate, Ms. Kepplinger asked session attendees to "keep your eye on" the Applicant Quality Submission (AQS) provision, since this is the one provision of the bill that the Patent Office really wants.  Ms. Kepplinger concluded by stating that the provision was one that "you may want to have your voice heard."

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

• "Docs at BIO: Representatives from JPO, EPO, SIPO, and USPTO Discuss Recent Developments in Japan, Europe, China, and the U.S.," June 22, 2008
• "Docs at BIO: Steve Burrill’s State of the Biotechnology Industry Report 2008," June 19, 2008
• "Patent Office Publishes Notice Regarding Impact of Proposed Markush Claims Rules on Small Entities," March 10, 2008