Patent Docs

ACI FDA Boot Camp

American Conference Institute (ACI) will be holding the next session of its FDA Boot Camp conference on September 17-18, 2013 in Boston, MA.  ACI faculty will help attendees:

• Master the basics of the application and approval processes for drugs, biologics, and devices
• Comprehend the structure of the FDA and the roles of the three major agency centers:  CDER, CBER, and CDHR
• Develop a practical working knowledge of clinical trials for drugs and biologics and the clearance process for devices
• Learn how devices are classified, monitored, and regulated
• Appreciate the complexities of pharmaceutical IP and the regulatory balance between brand name and generic products
• Recognize the pivotal role of labeling in the drug and biologics approval process
• See the importance of cGMPs to the post-approval regulatory process
• Navigate the protocols of adverse events monitoring, signal detection, product withdrawals, and recalls

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

• The Basics: Understanding and Working with the FDA -- Jurisdiction, Functions, Organization, and Operations
• The Nature of the Approval Process
• Understanding the Clinical Trial Process for Drugs and Biologics
• Obtaining and Challenging Market Exclusivity for Drug Products and Biologic Products: IP Protection, Data Exclusivity, Trademark and Brand Protection, Hatch-Waxman, BPCIA, and More:
• Part 1 -- Overview of Patent and Trademark Issues
• Part 2 -- Hatch-Waxman and BPCIA Overview
• Drugs and Biologics: Labeling
• cGMPs: Drugs and Biologics (Current Good Manufacturing Practices)
• Adverse Events Monitoring, Pharmacovigilance and Risk Management
• Medical Devices: Classifications, the Essentials of the Premarket Review Process, and Post-Market Requirements and Concerns
• Recall Guidance for Drugs, Biologics, and Medical Devices: What You Need to Know

A pre-conference workshop on the "Fundamentals of FDA Regulatory Law" and "Resolving Ethical Challenges Encountered During the Drug Approval Process" will be offered on September 16, 2013 from 1:00 to 5:00 pm.  The first part of the workshop will provide a basic overview of FDA regulations and will prepare attendees for the in-depth discussions that will take place throughout the conference, and explore ethical issues that may arise in the context of communications with FDA on behalf of clients.  The second part of the workshop will explore ethical issues that may arise in the context of communications with FDA on behalf of clients.

Two post-conference master classes will be offered on September 18, 2013.  The first master class, entitled "Hatch-Waxman and BPCIA: Overview of Biosimilars and Life Cycle Planning for Drugs and Biologics," will provide an in-depth overview of biosimilars as well as analyses of bioequivalence and exclusivities and their role in patent and product life cycle management.  The second master class, entitled "Post-Approval Marketing Guidance and Preemption Protocols," will address issues that arise post-approval, including advertising, promotion, and off-label promotion and enforcement, as well as preemption fundamentals.

An agenda for the conference can be found here.  A complete brochure for this conference, including an agenda, detailed descriptions of conference sessions, list of speakers, and registration form can be obtained here.

The registration fee is $2,295 (conference alone), $2,895 (conference and workshop or conference and one master class), or $3,295 (conference, workshop, and one master class).  Those registering by July 19, 2013 will receive a $300 discount and those registering by August 16, 2013 will receive a $200 discount.  Patent Docs readers who reference the discount code "PD 200" will receive $200 off the current price tier when registering.  Those interested in registering for the conference can do so here, by e-mailing [email protected], by calling 1-888-224-2480, or by faxing a registration form to 1-877-927-1563.

Patent Docs is a media partner of ACI's FDA Boot Camp conference.

CLE on AMP v. Myriad

Law Seminars International (LSI) will be offering a one-hour telebriefing on "The Myriad Decision: Practical Implications for Biotechnology Companies Protecting IP Assets" on July 17, 2013 from 3:00 to 4:00 pm (Eastern).  Dr. Barbara R. Rudolph of Finnegan Henderson Farabow Garrett & Dunner LLP will moderate a panel that includes Jennifer L. Swize of Jones Day and Courtenay C. Brinckerhoff of Foley & Lardner LLP.  The panel will discuss the Myriad decision and the possible implications for patent procurement, patent litigation, the biotechnology industry, and the future of medical research.  Among the topics to be covered are:

• Impact of the Myriad Decision on patents for genetic research
• How the decision distinguishes between natural and synthetic gene sequences
• Legal and business implications for the biotech industry
• New strategies for protecting DNA-based intellectual property moving forward

A Q&A will follow the presentation and last for up to 30 minutes.

The registration fee is $150 per caller and $100 for each additional person on the same line who desires continuing education credit.  Those interested in registering for the telebriefing, can do so here.

Webinar on Inducement to Infringe in Hatch-Waxman Litigation

Strafford will be offering a webinar/teleconference on "Inducement to Infringe in Hatch-Waxman Litigation: Lessons from Commil USA v. Cisco Systems and Bayer Schering v. Lupin for Pharma Patents" on August 21, 2013 from 1:00 to 2:30 pm (EDT).  Thomas L. Irving, Dr. David P. Frazier, and Robert F. Shaffer of Finnegan Henderson Farabow Garrett & Dunner provide patent counsel with guidance on claim and label language; to proactively coordinate patent, regulatory and clinical personnel; and to maintain consistency between claims and likely or actual label language throughout patent prosecution and label negotiation with the FDA.  The webinar will review the following questions:

• What can be learned from the AstraZeneca v. Apotex, Bayer Schering v. Lupin, and Commil USA v. Cisco Systems Inc. decisions?
• What are the best approaches to maintain consistency between claims and likely or actual label language?
• What steps can be taken to maintain the coordination of patent, regulatory and clinical personnel throughout the patent prosecution and label negotiation with the FDA?

The registration fee for the webinar is $297 ($362 for registration and CLE processing).  Those registering by July 26, 2013 will receive a $50 discount.  Those interested in registering for the webinar, can do so here.

European Biotech Patent Law Webinar

D Young & Co will be offering its next European biotech patent law update on July 17, 2013.  The 45-minute webinar will be offered at three times: 4:00 am, 7:00 am, 12:00 pm (EDT). D Young & Co European Patent Attorneys Robert Dempster and Simon O'Brien will provide an essential update and live Q&A on EPO biotechnology case law.

While there is no fee to participate, attendees must register in advance.  Those wishing to register can do so here.

Webinar on Implications of CLS Bank Int'l v. Alice Corp.

McDonnell Boehnen Hulbert & Berghoff LLP will be offering a live webinar entitled "What are the Implications of CLS Bank Int'l v. Alice Corp. on Computer-Implemented Inventions?" on August 22, 2013 from 10:00 am to 11:15 am (CT).  MBHB attorney Rory P. Shea will cover the potential implications of the CLS Bank decision on claims directed to computer-implemented inventions.  Topics to be covered include:

• A review of the CLS Bank decision and the takeaways from that decision
• A review of how courts are interpreting and applying the CLS Bank decision since it was handed down
• A discussion of how the CLS Bank decision may impact the prosecution and litigation of claims directed to computer-implemented inventions going forward

While there is no fee to participate, attendees must register in advance.  Those wishing to register can do so here.  CLE credit is pending for the states of California, Georgia, Illinois, North Carolina, New Jersey, New York and Virginia.

Manufacturing Innovation in America Act Introduced in House

By Donald Zuhn --

On June 28, Rep. Allyson Schwartz (D-PA) introduced legislation (H.R. 2605) to amend the Internal Revenue Code of 1986 to allow a deduction for "patent box" profit from the use of U.S. patents (and foreign patents in certain circumstances).  The bill, also known as the Manufacturing Innovation in America Act of 2013, is identical to legislation that Rep. Schwartz introduced last year.  The term "patent box" refers to a tax incentive that provides a reduced tax rate on profits derived from products that incorporate patents.  The tax incentive is known as a "patent box" because there is a box for patent profits to check on the tax form.

In a press release that was issued when the legislation was introduced last year, Rep. Schwartz (at left) noted that while the U.S. "leads the world in innovation and research and development,  . . . our current tax code fails to reflect the challenges of a competitive global economy, especially as it relates to domestic manufacturing."  According to Rep. Schwartz, the legislation she introduced would "further incentivize innovation, research and development, and manufacturing in the United States [by] reduc[ing] business taxes by more than half, to a 10 percent rate, for companies that manufacture patented products in the United States," thereby "lead[ing] to both U.S. and foreign companies bringing jobs back to the United States, as well as the creation of new jobs."  Her co-sponsor last year, Rep. Charles Boustany, Jr. (R-LA) -- who has yet to sign on to the bill this year -- noted last year that:

As the global economy continues to grow, the emergence of tools, such as ‘Patent Boxes,’ seek to drive domestic research and development while creating cutting-edge technologies.  Aimed to retain home-grown innovation, these tools allow for countries to promote domestic talent and incentivize companies to expand.  America should look toward engaging in this practice as well.  This tax rate reduction will lead to job creation across the country in sectors ranging from life-saving medical technology development, to next-generation energy technologies.

Biogen Idec Vice-President Lynne Sullivan indicated that the "legislation takes an important step towards making the U.S. corporate tax system globally competitive, and will drive domestic job growth in research and development and high-tech manufacturing."

Rep. Schwartz explained that the bill would provide a 10% tax rate on the sale of qualifying patented products by American businesses.  Among the business sectors that she expects to benefit from the legislation are the pharmaceutical and biotechnology sectors.  According to Rep. Schwartz, in order for a company to qualify for the reduced tax rate, the company must have a U.S. patent, and a substantial portion of the patents covering the product must be the result of research and development performed in the U.S.  The legislation specifies that a foreign patent may also be treated as a "qualified patent" under the bill if the foreign patent is "for the same or substantially similar invention or application" as a U.S. patent that the taxpayer holds or exclusively licenses, and provided that the taxpayer holds or exclusively licenses the foreign patent.  The bill's definitions of patent box profit, IP profit, routine profit, allocation method, patent gross receipts, and qualified patent property fall well outside the scope of this blog, so readers (and tax attorneys) who are interested in obtaining more details should consult the bill itself.

Noting that "[o]ur global economic competitors -- including China, France, Spain and soon the United Kingdom -- have tax rates varying from 5 to 10 percent on the income generated from patents or other types of intellectual property," Rep. Schwartz believes that H.R. 2605 would fix "an outdated tax code that doesn't reflect our 21st century innovation economy," and encourage companies who conduct research an product development in the U.S. to also establish manufacturing operations in this country, rather than overseas.

After being introduced, the bill was referred to the House Committee on Ways and Means.

Myriad Genetics Files Infringement Suit Against Gene by Gene for Genetic Diagnostic Testing of BRCA Genes

By Kevin E. Noonan --

A day after Myriad Genetics sued Ambry Genetics for patent infringement, the company filed suit in the District of Utah, Central Divisions against Gene by Gene Ltd. (Case No. 2:13-cv-00643-EJF; complaint).  The complaint is nearly identical to Myriad's complaint against Ambry Genetics, and once again Myriad is joined by the University of Utah Research Foundation, the Trustees of the University of Pennsylvania, HSC Research and Development Limited Partnership, and Endorecherche Inc.

This Complaint alleges that:

Defendant, through its DNA Traits division, began offering its BRCA1 and BRCA2 analysis as part of its testing menu on June 13, 2013.  Defendant offers stand-alone tests comprising full gene sequencing and analyses for the BRCA 1 and BRCA 2 genes.

Defendant is infringing, contributing to the infringement of, and/or inducing others to infringe [each of the nine asserted patents] by making, manufacturing, promoting, marketing, advertising, distributing, offering for sale and selling and/or causing to be offered or sold BRCA1 and BRCA2 products that infringe at least the following claim of [each of the patents in suit] literally and/or under the doctrine of equivalents [].

The specific claims Myriad alleges are infringed include the following:  claim 6 of U.S. Patent No. 5,709,999; claims 6, 16 and 17 of  U.S. Patent No. 5,747,282; claims 7, 8, 12, 23, and 26 of U.S. Patent No. 5,753,441; claims 29 and 30 of U.S. Patent No. 5,837,492; claim 4 of U.S. Patent No. 6,033,857; claims 2, 3 and 4 of U.S. Patent No. 5,654,155; claims 2, 3, 4, 5, 6, and 7 of U.S. Patent No. 5,750,400; claim 5 of U.S. Patent No. 6,951,721; and claims 3, 4, 5, 6, 7, 8, 11, 14, 17, 18, 19 of U.S. Patent No. 7,250,497.  Missing from the complaint against Gene by Gene are allegations of infringement of claims 32 and 33 of U.S. Patent No. 6,051,379 asserted in the complaint Myriad filed yesterday against Ambry Genetics.

Once again, Myriad and its co-plaintiffs request judgment of patent infringement, an injunction, an accounting and damages, delivery for destruction of all "products" that infringe any of the asserted claims, a finding of willful infringement, and a request for attorneys' fees, enhanced damages and costs of suit, as well as a jury trial.

The genetic diagnostics community awaits the identity of the next of its members who announced plans to market BRCA gene testing that Myriad decides to sue.  It appears that Myriad is serious about protecting its intellectual property until the company's patents expire over the next few years.

Fresenius USA, Inc. v. Baxter International, Inc. (Fed. Cir. 2013)

By Alison Baldwin --

Just before the July 4th holiday, the Federal Circuit issued its ruling in Fresenius USA, Inc. v. Baxter International, Inc. ("Fresenius II").  The Federal Circuit framed the question at issue as:  "Whether under the reexam statute, the cancellation of claims by the PTO is binding in pending district court infringement litigation."  But the question likely at issue for most practitioners in reviewing the case is "When is the district court's determination considered 'final'?"

The case has a long history dating back to 2003 when Fresenius filed suit seeking a declaratory judgment of invalidity of three Baxter patents, including claims 26-31 of the U.S. Patent No. 5,247,434 patent (the only patent and claims relevant to the present discussion).  In 2007, the District Court granted Baxter's motion for JMOL, finding that Fresenius has presented insufficient evidence to support the jury's verdict of invalidity of the '434 patent.  Fresenius Med. Care Holdings, Inc. v. Baxter Int'l, Inc., No. 03-CV-1431, 2007 WL 518804 (N.D. Cal. Feb. 13, 2007).  The Federal Circuit  affirmed the District Court on the issue of validity with respect to the '434 patent, but vacated the District Court's injunction and post verdict royalty awards and remanded the case back to the District Court regarding those issues.  Fresenius USA, Inc. v. Baxter Int'l, Inc., 582 F.3d 1288 (Fed. Cir. 2009) ("Fresenius I").  In March of 2012, the District Court awarded Baxter post verdict damages at a reduced royalty rate and entered final judgment.  Fresenius USA, Inc. v. Baxter Int'l, Inc., No. 03-CV-1431, 2012 WL 761712 (N.D. Cal. Mar. 8, 2012).

However, the execution of this final judgment was stayed by the District Court, because while the litigation was ongoing in the District Court, an ex parte reexamination of the '434 patent was occurring in parallel in the U.S. Patent Office.  In 2005, two years after filing the declaratory judgment case in the District Court, Fresenius also filed a request for ex parte reexamination of the same claims of the '434 patent.  In December 2007, the examiner entered a final rejection finding claims 26-31 of the '434 patent invalid as obvious.  This determination was affirmed by the Board of Patent Appeals and Interferences in March of 2010.  Ex parte Baxter, Int'l, Inc., No. 2009-006493, 2010 WL 1048980 (B.P.A.I. Mar. 18, 2010).  The BPAI determination was affirmed by the Federal Circuit in May 2012.  In re Baxter Int'l, Inc., 678 F.3d 1357 (Fed. Cir. 2012).  Thus, we now have Baxter prevailing before the District Court and Fresenius prevailing at the USPTO, setting the stage for the present appeal to determine which party would ultimately prevail.  For the majority of the panel, the winner is Fresenius.  For Judge Newman, the winner should have been Baxter.

Much of the discussion by the Court focuses on the history of the reissue and reexamination statutes.  However, everyone (even Baxter and dissenting Judge Newman) agrees that in general, when a claim is cancelled through reissue or reexamination, the patentee loses any cause of action based on that claim, and any pending litigation in which the claims are asserted becomes moot.  Where the real dispute lies is whether or not the USPTO's cancellation of claims 26-31 of the '434 patent should be given weight at this point in the District Court litigation.

The majority held that the USPTO's cancellation of the '434 patent claims rendered the District Court's judgment moot because neither the 2007 entry of judgment by the District Court, the remand decision by the Federal Circuit in Fresenius I, nor the District Court's 2012 entry of judgment was "sufficiently final."  Fresenius II at 20.  The Court distinguished the finality of a judgment for purposes of determining res judicata from the finality of a judgment for purposes of immunity from the effect of the final judgment in the PTO proceedings.  Id. at 19.  While the District Court's 2007 judgment was final for purposes of appeal and might have been given preclusive effect in another infringement case between the parties, the Court held that "it was not sufficiently final to preclude application of the intervening final judgment" in a reexamination proceeding.  Id.  Furthermore, while the Federal Circuit's decision in Fresenius I affirmed the validity of the '434 patent, the Court held that this was also not sufficiently final to provide immunity from the intervening final judgment of the reexamination because the issue of post-judgment damages had been remanded back to the District Court.  Id. at 20.  The Court followed a traditional analysis of finality wherein if any issue of law or fact remains, such as the issue of post-judgment damages in this case, then the decision is not final for purposes of preclusion.  Id. at 20-21.

In her dissent, Judge Newman took issue with the majority's view of finality.  In her opinion, the Federal Circuit's decision in Fresenius I resolved all issues of patent validity and created judicial finality.  Fresenius II (Dissent at 12).  Judge Newman opined that finality and preclusion should be imposed as to issues that were finally decided in full and fair litigation.  Id. at 16.  "[T]he issue of validity of the '434 patent had been raised, litigated, and decided, with full participation of the accused infringer; it cannot be relitigated."  Id. at 14.  The majority would agree, the issue of validity of the '434 patent cannot be relitigated -- but, in their view, it can definitely still be trumped.

Fresenius USA, Inc. v. Baxter International, Inc. (Fed. Cir. 2013)
Panel: Circuit Judges Newman, Dyk, and Prost
Opinion for the Court by Circuit Judge Dyk; dissenting opinion by Circuit Judge Newman

Myriad Genetics Files Suit Against Ambry Genetics for Genetic Diagnostic Testing of BRCA Genes

By Kevin E. Noonan --

Today Myriad Genetics sued Ambry Genetics, Corp. in the District of Utah, Central Division for patent infringement of ten patents relating to genetic diagnostic testing (Case No. 2:13-cv-00640-RJS; complaint).  Ambry Genetics was one of the first companies to announce that it would provide genetic diagnostic testing for the BRCA 1 and BRCA 2 genes on the day the U.S. Supreme Court announced its decision in AMP v. Myriad Genetics on the question of "whether human genes are patentable."  Joining Myriad as plaintiffs are the University of Utah Research Foundation, the Trustees of the University of Pennsylvania, HSC Research and Development Limited Partnership, and Endorecherche Inc.

The Complaint alleges that:

Defendant began offering its BRCA1 and BRCA2 analysis as part of its cancer testing menu on June 13, 2013.  On information and belief, Defendant offers stand-alone tests comprising full gene sequencing and deletion/duplication analyses for the BRCA 1 and BRCA 2 genes.  On information and belief, Defendant also offers full gene sequencing and deletion/duplication analyses for the BRCA 1 and BRCA 2 genes as part of multiple hereditary cancer panels that test cancer susceptibility using next-generation sequencing technology.

Defendant is infringing, contributing to the infringement of, and/or inducing others to infringe the '999 patent by making, manufacturing, promoting, marketing, advertising, distributing, offering for sale and selling and/or causing to be offered or sold certain BRCA1, BRCA2, BRCAPlus, BreastNext, OvaNext, and CancerNext products that infringe at least the following claim of [each of the patents in suit] literally and/or under the doctrine of equivalents for ten patents owned or licensed to Myriad.

The specific claims Myriad alleges are infringed include the following:

First Claim for Relief:  U.S. Patent No. 5,709,999

Claim 6: A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 12A, 14, 18 or 19 in a human which comprises analyzing a sequence of a BRCA1 gene or BRCA1 RNA from a human sample or analyzing a sequence of BRCA1 cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:1, wherein a germline alteration is detected by amplifying all or part of a BRCA1 gene in said sample using a set of primers specific for a wild-type BRCA1 gene to produce amplified BRCA1 nucleic acids and sequencing the amplified BRCA1 nucleic acids.

Second Claim for Relief: U.S. Patent No. 5,747,282

Claim 6: An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2,  wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1, and having at least 15 nucleotides of the DNA of claim 2.

Claim 16: A pair of single-stranded DNA primers for determination of a nucleotide sequence of a BRCA1 gene by a polymerase chin reaction, the sequence of said primers being derived from human chromosome 17q, wherein the use of said primers in a polymerase chain reaction results in the synthesis of DNA having all or part of the sequence of the BRCA1 gene.

Claim 17: The pair of primers of claim 16 wherein said BRCA1 gene has the nucleotide sequence set forth in SEQ ID NO:1.

Third Claim for Relief: U.S. Patent No. 5,753,441

Claim 7: A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject, wherein a germline nucleic acid sequence is compared by hybridizing a BRCA1 gene probe which specifically hybridizes to a BRCA1 allele to genomic DNA isolated from said sample and detecting the presence of a hybridization product wherein a presence of said product indicates the presence of said allele in the subject.

Claim 8: A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject, wherein a germline nucleic acid sequence is compared by amplifying all or part of a BRCA1 gene from said sample using a set of primers to produce amplified nucleic acids and sequencing the amplified nucleic acid.

Claim 12: A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject, wherein a germline nucleic acid sequence is compared by amplifying BRCA1 nucleic acids from said sample to produce amplified nucleic acids, hybridizing the amplified nucleic acids to a BRCA1 DNA probe specific for a BRCA1 allele and detecting the presence of a hybridization product, wherein the presence of said product indicates the presence of said allele in the subject.

Claim 23. A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 11 and 12 which comprises analyzing a sequence of the BRCA1 gene or BRCA1 RNA from a human sample or analyzing the sequence of BRCA1 CDNA made from mRNA from said sample, wherein a germline alteration is detected by amplifying all or part of a BRCA1 gene in said sample using a set of primers to produce amplified nucleic acids and sequencing the amplified nucleic acids.

Claim 26.  A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 11 and 12 which comprises analyzing a sequence of the BRCA1 gene or BRCA1 RNA from a human sample or analyzing the sequence of BRCA1 CDNA made from mRNA from said sample, wherein a germline alteration is detected by amplifying BRCA1 gene nucleic acids in said sample, hybridizing the amplified nucleic acids to a BRCA1 DNA probe specific for one of said alterations and detecting the presence of a hybridization product, wherein the presence of said product indicates the presence of said alteration.

Fourth Claim for Relief: U.S. Patent No. 5,837,492

Claim 29. A pair of single-stranded DNA primers of at least 15 nucleotides in length for determination of the nucleotide sequence of a BRCA2 gene by a polymerase chain reaction, the sequence of said primers being isolated from human chromosome 13, wherein the use of said primers in a polymerase chain reaction results in the synthesis of DNA comprising all or at least 15 contiguous nucleotides of the BRCA2 gene.

Claim 30. The pair of primers of claim 29 wherein said BRCA2 gene has the nucleotide sequence set forth in SEQ ID NO:1.

Fifth Claim for Relief: U.S. Patent No. 6,033,857

Claim 4. A method for diagnosing a predisposition for breast cancer in a human subject which comprises comparing the germline sequence of the BRCA2 gene or the sequence of its mRNA in a tissue sample from said subject with the germline sequence of the wild-type BRCA2 gene or the sequence of its mRNA, wherein an alteration in the germline sequence of the BRCA2 gene or the sequence of its mRNA of the subject indicates a predisposition to said cancer, wherein the detection in the alteration in the germline sequence is determined by an assay selected from the group consisting of (a) observing shifts in electrophoretic mobility of single-stranded DNA on non-denaturing polyacrylamide gels, (b) hybridizing a BRCA2 gene probe to genomic DNA isolated from said tissue sample, (c) hybridizing an allele-specific probe to genomic DNA of the tissue sample, (d) amplifying all or part of the BRCA2 gene from said tissue sample to produce an amplified sequence and sequencing the amplified sequence, (e) amplifying all or part of the BRCA2 gene from said tissue sample using primers for a specific BRCA2 mutant allele, (f) molecularly cloning all or part of the BRCA2 gene from said tissue sample to produce a cloned sequence and sequencing the cloned sequence, (g) identifying a mismatch between (1) a BRCA2 gene or a BRCA2 mRNA isolated from said tissue sample, and (2) a nucleic acid probe complementary to the human wild-type BRCA2 gene sequence, when molecules (1) and (2) are hybridized to each other to form a duplex, (h) amplification of BRCA2 gene sequences in said tissue sample and hybridization of the amplified sequences to nucleic acid probes which comprise wild-type BRCA2 gene sequences, (i) amplification of BRCA2 gene sequences in said tissue sample and hybridization of the amplified sequences to nucleic acid probes which comprise mutant BRCA2 gene sequences, (j) screening for a deletion mutation in said tissue sample, (k) screening for a point mutation in said tissue sample, (l) screening for an insertion mutation in said tissue sample, (m) in situ hybridization of the BRCA2 gene of said tissue sample with nucleic acid probes which comprise the BRCA2 gene.

Sixth Claim for Relief: U.S. Patent No. 5,654,155

Claim 2. A method of identifying individuals having a BRCA1 gene with a BRCA1 coding sequence not associated with breast or ovarian cancer comprising:
    a) amplifying a DNA fragment of an individual's BRCA1 coding sequence using an oligonucleotide primer which specifically hybridizes to sequences within the gene;
    b) sequencing said amplified fragment by dideoxy sequencing;
    c) repeating steps (a) and (b) until said individual's BRCA1 coding sequence is completely sequenced;
    d) comparing the sequence of said amplified DNA to the sequence of SEQ. ID. NO: 1;
    e) determining the presence or absence of each of the following polymorphic variations in said individual's BRCA1 coding sequence:
    AGC and ACT at position 2201, TTG and CTG at position 2430,  CCG and CTG at position 2731,  GAA and GGA at position 3232, AAA and AGA at position 3667, TCT and TCC at position 4427, and ACT and GGT at position 4956;
    f) determining any sequence differences between said individual's BRCA1 coding sequences and SEQ. ID. NO: 1 wherein the presence of any of the said polymorphic variations and the absence of a polymorphism outside of positions 2201, 2430, 2731, 3232, 3667, 4427, and 4956, is correlated with an absence of increased genetic susceptibility to breast or ovarian cancer resulting from a BRCA1 mutation in the BRCA1 coding sequence.

Claim 3. A method according to claim 2 wherein said oligonucleotide primer is labeled with a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label or an enzyme label

Claim 4. A method of detecting an increased genetic susceptibility to breast and ovarian cancer in an individual resulting from the presence of a mutation in the BRCA1 coding sequence, comprising:
    a) amplifying a DNA fragment of an individual's BRCA1 coding sequence using an oligonucleotide primer which specifically hybridizes to sequences within the gene;
    b) sequencing said amplified fragment by dideoxy sequencing;
    c) repeating steps (a) and (b) until said individual's BRCA1 coding sequence is completely sequenced;
    d) comparing the sequence of said amplified DNA to the sequence of SEQ. ID. NO: 1;
    e) determining any sequence differences between said individual's BRCA1 coding sequences and SEQ. ID. NO: 1 to determine the presence or absence of polymorphisms in said individual's BRCA coding sequences wherein a polymorphism which is not any of the following:
    AGC or AGT at position 2201, TTG or CTG at position 2430, CCG or CTG at position 2731, GAA or GGA at position 3232, AAA or AGA at position 3667, TCT or TCC at position 4427, and AGT or GGT at position 4956;
    is correlated with the potential of increased genetic susceptibility to breast or ovarian cancer resulting from a BRCA1 mutation in the BRCA1 coding sequence.

Seventh Claim for Relief: U.S. Patent No. 5,750,400

Claim 2. A method of identifying individuals having a BRCA1 gene with a BRCA1 coding sequence not associated with ovarian or breast cancer disease, comprising:
    (a) amplifying a DNA fragment of an individual's BRCA1 coding sequence using an oligonucleotide primer which specifically hybridizes to sequences within the gene;
    (b) sequencing said amplified DNA fragment by dideoxy sequencing;
    (c) repeating steps (a) and (b) until said individual's BRCA1 coding sequence is completely sequenced;
    (d) comparing the sequence of said amplified DNA fragment to a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5;
    (e) determining the presence or absence of each of the following polymorphic variations in said individual's BRCA1 coding sequence:
        (i) C and T at position 2201,
        (ii) T and C at position 2430,
        (iii) C and T at position 2731,
        (iv) A and G at position 3232,
        (v) A and G at position 3667,
        (vi) T and C at position 4427, and
        (vii) A and G at position 4956;
    (f) determining any sequence differences between said individual's BRCA1 coding sequences and a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5, wherein the presence of said polymorphic variations and the absence of a variation outside of positions 2201, 2430, 2731, 3232, 3667, 4427 and 4956 is correlated with an absence of increased genetic susceptibility to breast or ovarian cancer resulting from a BRCA1 mutation in the BRCA1 coding sequence.

Claim 3. A method of identifying individuals having a BRCA1 gene with a BRCA1 coding sequence not associated with ovarian or breast cancer disease, comprising:
    (a) amplifying a DNA fragment of an individual's BRCA1 coding sequence using an oligonucleotide primer which specifically hybridizes to sequences within the gene;
    (b) sequencing said amplified DNA fragment by dideoxy sequencing;
    (c) repeating steps (a) and (b) until said individual's BRCA1 coding sequence is completely sequenced;
    (d) comparing the sequence of said amplified DNA fragment to a BRCA1^(omi)) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5;
    (e) determining the presence or absence of each of the following polymorphic variations in said individual's BRCA1 coding sequence:
        (i) C and T at position 2201,
        (ii) T and C at position 2430,
        (iii) C an d T at position 2731,
        (iv) A and G at position 3232,
        (v) A and G at position 3667,
        (vi) T and C at position 4427, and
        (vii) A and G at position 4956; and
    (f) determining any sequence differences between said individual's BRCA1 coding sequences and a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5, wherein the presence of said polymorphic variations and the absence of a variation outside of positions 2201, 2430, 2731, 3232, 3667, 4427 and 4956 is correlated with an absence of increased genetic susceptibility to breast or ovarian cancer resulting from a BRCA1 mutation in the BRCA1 coding sequence;
    wherein codon variations occur at the following frequencies, respectively, in a Caucasian population of individuals with no family history of breast or ovarian cancer:
        (i) at position 2201, C and T occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (ii) at position 2430, T and C occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (iii) at position 2731, C and T occur at frequencies from about 25 to about 35%, and from about 65 to about 75%, respectively;
        (iv) at position 3232, A and G occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (v) at position 3667, A and G occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (vi) at position 4427, T and C occur at frequencies from about 45 to about 55%, and from about 45 to about 55%, respectively; and
        (vii) at position 4956, A and G occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively.

Claim 4. A method according to claims 2 or 3, wherein said oligonucleotide primer is labeled with a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, or an enzyme label.

Claim 5. A method of detecting an increased genetic susceptibility to breast and ovarian cancer in an individual resulting from the presence of a mutation in the BRCA1 coding sequence, comprising:
    (a) amplifying a DNA fragment of an individual's BRCA1 coding sequence using an oligonucleotide primer which specifically hybridizes to sequences within the gene;
    (b) sequencing said amplified DNA fragment by dideoxy sequencing;
    (c) repeating steps (a) and (b) until said individual's BRCA1 coding sequence is completely sequenced;
    (d) comparing the sequence of said amplified DNA fragment to a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5;
    (e) determining any sequence differences between said individual's BRCA1 coding sequences and a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ. ID. NO.: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5 in order to determine the presence or absence of base changes in said individual's BRCA1 coding sequence wherein a base change which is not any one of the following:
        (i) C and T at position 2201,
        (ii) T and C at position 2430,
        (iii) C and T at position 2731,
        (iv) A and G at position 3232,
        (v) A and G at position 3667,
        (vi) T and C at position 4427, and
        (vii) A and G at position 4956, is correlated with the potential of increased genetic susceptibility to breast or ovarian cancer resulting from a BRCA1 mutation in the BRCA1 coding sequence.

Claim 6. A method of detecting an increased genetic susceptibility to breast and ovarian cancer in an individual resulting from the presence of a mutation in the BRCA1 coding sequence, comprising:
    (a) amplifying a DNA fragment of an individual's BRCA1 coding sequence using an oligonucleotide primer which specifically hybridizes to sequences within the gene;
    (b) sequencing said amplified DNA fragment by dideoxy sequencing;
    (c) repeating steps (a) and (b) until said individual's BRCA1 coding sequence is completely sequenced;
    (d) comparing the sequence of said amplified DNA fragment to a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5;
    (e) determining any sequence differences between said individual's BRCA1 coding sequences and a BRCA1^(omi) DNA sequence selected from the group consisting of: SEQ ID NO: 1 together with SEQ ID NO: 3, SEQ ID NO: 1 together with SEQ ID NO: 5, SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 1 together with SEQ ID NO: 3 together with SEQ ID NO: 5, SEQ ID NO: 3 and SEQ ID NO: 5 in order to determine the presence or absence of base changes in said individual's BRCA1 coding sequence wherein a base change which is not any one of the following:
        (i) C and T at position 2201,
        (ii) T and C at position 2430,
        (iii) C and T at position 2731,
        (iv) A and G at position 3232,
        (v) A and G at position 3667,
        (vi) T and C at position 4427, and
        (vii) A and G at position 4956, is correlated with the potential of increased genetic susceptibility to breast or ovarian cancer resulting from a BRCA1 mutation in the BRCA1 coding sequence, wherein codon variations occur at the following frequencies, respectively, in a Caucasian population of individuals with no family history of breast or ovarian cancer:
        (i) at position 2201, C and T occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (ii) at position 2430, T and C occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (iii) at position 2731, C and T occur at frequencies from about 25 to about 35%, and from about 65 to about 75%, respectively;
        (iv) at position 3232, A and G occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (v) at position 3667, A and G occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively;
        (vi) at position 4427, T and C occur at frequencies from about 45 to about 55%, and from about 45 to about 55%, respectively; and
        (vii) at position 4956, A and G occur at frequencies from about 35 to about 45%, and from about 55 to about 65%, respectively.

Claim 7. A method according to claims 5 or 6, wherein said oligonucleotide primer is labeled with a radiolabel, a fluorescent label, a bioluminescent label, a chemiluminescent label, or an enzyme label.

Eighth Claim for Relief: U.S. Patent No. 6,051,379

Claim 32. A method of detecting a predisposition or higher susceptibility to cancer in an individual, comprising:
    (a) digesting DNA from an individual to obtain DNA fragments;
    (b) separating said DNA fragments;
    (c) detecting a DNA fragment containing nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909 of the BRCA2 gene sequence or a sequence variation at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909 of the BRCA2 gene sequence by sequencing;
    (d) comparing the sequence of said fragment with the BRCA2 gene sequence to determine the presence or absence of a sequence variation at nucleotide number 2192, 3772, 5193, 5374, 6495 or 6909, wherein the presence of a sequence variation indicates a predisposition or higher susceptibility to cancer.

Claim 33. A method according to claim 32 further comprising amplifying said DNA fragments prior to the detecting step (c).

Ninth Claim for Relief: U.S. Patent No. 6,951,721

Claim 5. A method for determining an omi haplotype of a human BRCA1 gene comprising: (a) determining the nucleotide sequence of the BRCA1 gene or fragment thereof from at least one female individual with a family history which indicates a predisposition to breast cancer, (b) comparing the determined nucleotide sequence from said female individual to SEQ ID NO: 263, and (c) determining the presence of the following nucleotide variations: thymine at nucleotides 2201 and 2731, cytosine at nucleotides 2430 and 4427, and guanine at nucleotides 3232, 3667 and 4956, wherein the presence of the nucleotide variations in the determined nucleotide sequence indicates the omi1 haplotype,  further comprising comparing the determined nucleotide sequence to SEQ ID NO: 265.

Tenth Claim for Relief: U.S. Patent No. 7,250,497

Claims 3, 4, 5, 6, 7, 8, 11, 14, 17, 18, 19

[Claim 1. An isolated nucleic acid comprising SEQ ID NO:6, and the complement thereof.

Claim 2. The isolated nucleic acid of claim 1, wherein said isolated nucleic acid comprises SEQ ID NO:37, or the complement thereof.]

Claim 3. A method of making the isolated nucleic acid of claim 2 comprising amplifying genomic DNA isolated from a sample obtained from a human patient.

Claim 4. A method of making the isolated nucleic acid of claim 1 comprising amplifying genomic DNA isolated from a sample obtained from a human patient.

Claim 5. The method of claim 4, wherein said sample is a blood sample.

Claim 6. The method of claim 4, wherein said amplification is by the polymerase chain reaction.

Claim 7. The method of claim 4, wherein said patient is being evaluated for an enhanced risk of cancer.

Claim 8. The method of claim 4, wherein said cancer is breast or ovarian cancer.

Claim 11. A method of making the isolated nucleic acid of claim 9 comprising amplifying genomic DNA isolated from a sample obtained from a human patient.

Claim 14. A method of making the isolated nucleic acid of claim 12 comprising amplifying genomic DNA isolated from a sample obtained from a human patient.

Claim 17. A method of making the isolated nucleic acid of claim 15 comprising amplifying genomic DNA isolated from a sample obtained from a human patient.

Claim 18. The isolated nucleic acid of claim 1, wherein said isolated nucleic acid comprises SEQ ID NO:41, or the complement thereof.

Claim 19. A method of making the isolated nucleic acid of claim 18 comprising amplifying genomic DNA isolated from a sample obtained from a human patient.

These method claims differ from the claims invalidated by the District Court in the Myriad case and affirmed by the Federal Circuit, which recited as limitations merely "comparing" an individual's BRCA gene sequence with the "normal" one, and thus Myriad is less likely to be estopped from asserting these claims against Ambry.

Myriad's Relief Requested in its complaint includes judgment of patent infringement, an injunction, an accounting and damages, delivery for destruction of all "products" that infringe any of the asserted claims, a finding of willful infringement, and a request for attorneys' fees, enhanced damages and costs of suit.  Myriad also demands a jury trial.

As has been discussed in earlier posts, some of these claims (e.g., directed to oligonucleotides) may be subject to invalidation on novelty grounds (see "Caught in a Time Warp: The (In)validity of BRCA1 Oligonucleotide Claims").  In addition, not all assignees are named in the complaint (most notably the U.S. Government "as represented by the Secretary of Health") and insofar as any of them are adjudged to be indispensible parties, any unwillingness to be joined might cause Myriad procedural difficulties.  But it is significant that Myriad has decided to assert these patents, and its continued ability to do so illustrates one of the generally unappreciated aspects of the Myriad case.  Plaintiffs in that case and their supporters, the ACLU and Public Patent Foundation, chose the claims against which to assert their challenge to the validity of Myriad's patents.  Which means, of course, that they chose not to challenge the claims Myriad is now asserting, leaving the plaintiffs (including breast cancer patients) without the full and complete remedy they no doubt were promised and that the press seems to believe the Supreme Court's June 13 decision gave them (see "Reaction to Supreme Court's Decision in AMP v. Myriad" and "Does the Myriad Decision Presage a Golden Age of Patent-Free Personalized Medicine?").  Instead, plaintiffs challenged claims to isolated DNA (characterized as "genes"), even though such claims are not infringed by the practice of modern genetic diagnostic methods.  The result of these strategic (and ultimately political or at least public-relations focused) decisions is that Myriad owns or has licensed patents that presumptively preclude Ambry Genetics or any other provider from offering BRCA gene-directed genetic diagnostic tests until these patents expire in the next few years.  In short, the parties are in exactly the same position that existed prior to the Myriad suit.  While this outcome should have been expected, it raises doubts about the consensus narrative of what "everybody knows" this case was all about.

BIO IP & Diagnostics Symposium

The Biotechnology Industry Organization (BIO) will be holding an IP & Diagnostics Symposium from 8:00 am to 2:45 pm on July 22, 2013 at the Hilton Alexandria Old Town Hotel in Alexandria, VA.  The Symposium will review the current patent law landscape and evaluate the impact on both the genetic diagnostics and biopharmaceutical sectors.  The program will review IP issues for diagnostics and companion diagnostics, and explore potential regulatory dimensions.  In hosting the event, BIO aims to inform industry and government alike on how to move the science forward in the current climate.  The Symposium will offer the following presentations and sessions:

• Keynote breakfast -- Jeffrey N. Peterson, Chief Executive Officer, Target Discovery, Inc.

• Session 1 -- Obtaining Patent Protection -- Patent Docs author Donald Zuhn of McDonnell Boehnen Hulbert & Berghoff LLP will moderate a panel including Mary Till, Legal Advisor, Office of Patent Legal Administration, U.S. Patent & Trademark Office; Duane Marks, Patent Counsel, Roche Diagnostics Operations, Inc.; and Patent Docs author Kevin Noonan of McDonnell Boehnen Hulbert & Berghoff LLP

• Session 2 -- Regulatory & Reimbursement -- Jennifer L. Fox of Brinks Hofer Gilson & Lione will moderate a panel including Sheila D. Walcoff, Founding Principal, Goldbug Strategies LLC

• Session 3 (Working Luncheon) -- Business Development & Strategic Deals -- Eric Steffe of Sterne Kessler Goldstein & Fox LLP will moderate a panel including Tim Shea of Sterne Kessler Goldstein & Fox LLP; Pia Maria Gargiulo, Managing Director, Companion Diagnostics, Precision for Medicine; Mollie Roth of PGx Consulting; and Zoran Zdraveski, Senior Director of Intellectual Property, Epizyme, Inc.

An agenda for the Symposium, including a list of speakers, moderators, and panelists can be obtained here.

Although there is no registration fee for the Symposium, space is limited and attendees must register for the program.  A registration form can be obtained here.  Additional information regarding the Symposium can be found on BIO's Patently Biotech blog.

Coalition of University TTOs File Amicus Brief in Lighting Ballast Control LLC v. Philips Electronics North America Corp.

By Kevin E. Noonan --

In his novel My Summer in a Garden (1870), Charles Dudley Warner famously said "Politics makes strange bedfellows."  That aphorism is illustrated once again in the joining of the Public Patent Foundation with eight technology transfer organizations and the Association of University of Technology Managers,* urging the Federal Circuit to overturn its decision in Cybor Corp. v. FAS Technologies, Inc., 138 F.3d 1448, 1456 (Fed. Cir. 1998) (en banc), that claim construction by a district court is entitled to no deference.

The brief (~7 page) amicus brief addresses the three questions posed by the Federal Circuit for en banc review:

1) Should [the] court overrule Cybor []?

2) Should [the] court afford deference to any aspect of a district court's claim construction?

3) If so, which aspects should be afforded deference?

As to the first question, the brief answers in the affirmative, simply stating that Cybor should be overruled to the extent it places factual determinations "outside the realm of deferential review" for reasons set forth in the remainder of the brief.

Regarding the second question, the brief notes that claim construction is a mixed question of law and fact, a situation not unusual in patent law, citing obviousness and enablement as being questions of law based on frequently disputed facts.  A district court's factual determination relating to these questions is reviewed under a "substantial evidence" standard (e.g., Martek Biosciences Corp. v. Nutrinova, Inc., 579 F.3d 1363, 1378 (Fed. Cir. 2009) (enablement); Honeywell Int'l, Inc. v. United States, 609 F.3d 1292, 1297 (Fed. Cir. 2010) (obviousness).  The brief also notes that the Supreme Court's decision in Markman v. Westview Instruments does not mandate the approach taken by the Federal Circuit in Cybor.  Even certain members of the Court (former Chief Judge Michel, current Chief Judge Rader) don't agree with the Court's approach in Cybor:

It seems to me that the claim construction question often cannot be answered without assessing, at least implicitly, what the average artisan knew and how she thought about the particular technology when the patent claims were written.  To make such determinations, the trial judge necessarily relies upon prior art documents and other evidence concerning the skill of the ordinary artisan at the relevant time.  Indeed, trial judges are arguably better equipped than appellate judges to make these factual determinations, especially in close cases.  In such instances, perhaps we should routinely give at least some deference to the trial court, given its greater knowledge of the facts.

Amgen Inc. v. Hoechst Marion Roussel, Inc., 469 F.3d 1039, 1041 (Fed. Cir. 2006) (Michel, C.J. and Rader, J., dissenting).

And other members of the Court have gone further, citing Fed. R. Civ. Pro. Rule 52(a); see Phillips v. AWH Corp., 415 F.3d 1303, 1332 (Fed. Cir. 2005) (en banc) (Mayer, J., and Newman, J., dissenting).  The TTO's amicus brief states:

The Amici agree with these dissenting opinions -- there is no reason to treat the appellate review of factual underpinnings related to claim construction any differently than any other factual determinations.  The resulting deference will ensure a greater predictability for the claim construction proceeding, and will avoid having to "re-try" the factual underpinnings of claim construction on appeal.

The advantages of adopting this standard of review would include "a greater predictability for the claim construction proceeding" and "avoid[ing] having to 're-try' the factual underpinnings of claim construction on appeal."  The resulting "[p]redictability and avoidance of duplicative effort are of particular importance to universities, related institutions, and the organizations to which such institutions belong," according to the brief, "particularly since patent litigation, with its attendant costs and uncertain outcome already places such institutions in a disadvantaged position."

Finally, the brief argues that a district court's factual determinations incident to claim construction should be reviewed under a "substantial evidence" standard.  The brief illustrates the consequences and justifications of their approach using the case at bar:

In resolving this question [i.e., the meaning of a disputed claim term], the district court evaluated evidence in the form of expert deposition testimony (and the parties' arguments thereon) regarding how persons skilled in the art would understand the limitation[].  After such evaluation, the district court found that such limitation indeed "corresponds to a class of structures."

The district court's finding regarding the meaning of [the disputed claim term] to those of ordinary skill in the art was indisputably one of fact.  The subject patent itself contained no evidence of how such hypothetical persons would understand that term, and the parties were consequently required to rely upon extrinsic evidence in the form of expert depositions in order to support their respective positions on the subject.  As with any other factual finding regarding claim construction, this factual finding is entitled to deference in the appellate review thereof.

One relevant argument in favor of discarding the claim construction analysis from Cybor is that in so doing the Federal Circuit might avoid the high percentage of reversals of district court claim construction (~30-40% according to some legal academics).  The counter-argument is that often, and perhaps the majority of the time, a district court's factual determinations can be dispositive of the claim construction exercise.  In these circumstances, giving even a "substantial evidence" level of deferential review to these factual determinations may vitiate any de novo review by the Federal Circuit of how the claims are properly construed as a matter of law.

The Federal Circuit is scheduled to hear the appeal en banc on September 13, 2013.

* The amici are: Association of University Technology Managers (AUTM), NUtech Ventures, Inc. (University of Nebraska – Lincoln), UNeMED Corporation (University of Nebraska Medical Center), STC.UNM (University of New Mexico), Wisconsin Alumni Research Foundation (University of Wisconsin), Colorado State University Research Foundation, Public Patent Foundation, Tec Edmonton (University of Alberta and City of Edmonton), The University of Pittsburgh of The Commonwealth System of Higher of Education, and Newsouth Innovations (University of New South Wales, Australia)

Hat tip to Gray on Claims for providing the amicus brief.

USPTO Files Reply Brief in Exelixis v. Rea

By Donald Zuhn --

At the end of June, the U.S. Patent and Trademark Office filed its reply brief with the Federal Circuit in Exelixis, Inc. v. Rea.  The appeal involves two decisions by the Eastern District of Virginia involving the impact of a Request for Continued Examination (RCE) on the calculation of patent term adjustment (PTA) for a patent, and in particular, on the amount of B-Delay an applicant can obtain after filing an RCE.  A discussion of the first decision to come out of the Eastern District of Virginia (Exelixis I), which was issued by Judge T. S. Ellis III on October 1, 2012, and which the USPTO has appealed, can be found here.  The opinion for the second decision (Exelixis II) -- which was issued by Judge Leonie M. Brinkema on January 28, 2013, and which Exelixis has appealed, can be found here.

The USPTO brief begins by noting that the Office's issue on appeal is:

[W]hether this Court should uphold the agency's longstanding interpretation of [35 U.S.C. § 154(b)(1)(B)(i)], under which any time consumed by an applicant's request for continued examination ("RCE") is excluded from the calculation of patent term adjustment under subsection 154(b)(1)(B) regardless of when the applicant filed the RCE.

While Exelixis argues that an RCE filed after the 3-year deadline (i.e., three years after the application was filed) should not impact the amount of B-Delay a patent can accrue, the USPTO argues that regardless of whether an RCE is filed before or after the 3-year deadline, a patent should not accrue B-Delay after the RCE is filed.  The Office summarizes Exelixis' issue on appeal as being:

[W]hether the Court should defer to the USPTO's definition of "any time consumed by continued examination of the application requested by the applicant under section 132(b)" to include all time elapsed between filing of an RCE and issuance of a patent.

In arguing that the Office's interpretation of the statute "avoids absurd results, realizes Congress's intent, and best makes sense of the provision as a whole," the USPTO brief notes that the District Court in Exelixis II "explained[ that] an RCE adds time to the processing of the application but delay after the filing of an RCE 'emanates solely from an applicant's original failure to file an application fit for a notice of allowance.'"  Therefore, the USPTO contends that the filing of an RCE is applicant-caused delay and not PTO-caused delay.  The brief argues that "although the statute is ambiguous, the USPTO's interpretation is by far the better reading of the statute and this Court should defer to it under Skidmore."

With respect to the ambiguity of the statute, the brief states that "the text of 35 U.S.C. § 154(b)(1)(B) is ambiguous," in that "[i]t can be read as providing that time associated with the filing of an RCE is excluded from the B-delay category of PTA, regardless of when the RCE is filed, or it can be read to apply only to RCEs filed within the first three years."  The brief asserts that "[r]eading the statute as a whole, the USPTO's interpretation is by far the better way to resolve this textual ambiguity."  Fearing that Exelixis' interpretation of the statute would permit submarine patents, the brief explains that "an applicant could file an overly broad patent application, repeatedly fail to address the examiner's reasons for rejection, and then narrow it only in a later RCE."

As for Exelixis' issue on appeal, the brief contends that:

The USPTO has discretion under Section 132(b) to define the RCE process and to determine when it is completed.  The USPTO has done so and determined that the RCE process continues until the patent is actually issued because, once an RCE is requested, "any further processing or examination of the application, including granting of a patent, is by virtue of the continued examination."

The brief notes that "Congress left it to the USPTO to define the process for 'continued examination' under Section 132(b), including when that process begins and ends."  And as the brief explains, the Office defined the process to be such that "[o]nce an RCE is requested, 'any further processing or examination of the application, including granting of a patent, is by virtue of the continued examination,'" meaning that "any time following the filing of an RCE is consumed by the RCE."

In response to Exelixis' argument that examination cannot include the period between the issuance of the notice of allowance and the issuance of the patent because the notice of allowance states that the application "has been examined" and no actual examination occurred after that time, the brief counters that:

In the patent context . . . the word "examination" is not limited in such a way.  The period of examination spans the entire time that the application is pending before the USPTO.  See 35 U.S.C. § 131 (indicating that issuance immediately follows examination).  This understanding of the term "examination" is consistent with the USPTO's regulation governing "adjustment of patent term due to examination delay," which includes patent term adjustment for delays in issuing the patent after payment of the issue fee.  See 37 C.F.R. § 1.703(a)(6) (emphasis added).  Likewise, late payment of the issue fee and requests to defer issuance of a patent after payment of the issue fee, both of which must occur after the notice of allowance is issued, represent a failure of the applicant to engage in reasonable efforts to conclude "processing or examination" of the application.

As for Exelixis' argument that it is unfair to deny an applicant PTA for time between the notice of allowance and the issue date because the USPTO controls the time it takes to issue a patent, the brief indicates that:

As an initial matter, this is only partially true.  The USPTO only controls the time after payment of the issue fee and satisfaction of any other outstanding requirements by the applicant.  The applicant controls the time it takes to pay the issue fee and fulfill any other necessary requirements.  In Exelixis II, it took Exelixis almost three months (from July 1 to September 30) to pay the issue fee, accounting for the majority of the time that elapsed between the notice of allowance and the patent issue date.  Even though Exelixis, not the USPTO, was responsible for that time, and Exelixis waited until the last day to pay the issue fee, Exelixis now requests PTA for the entire period and asserts that it is "time consumed by [the USPTO's] administrative delay."

(citation omitted).

The brief also notes that "PTA is . . . available where there are undue USPTO delays in issuing the patent [e.g., when the USPTO takes more than four months to issue a patent after the issue fee is paid]."  Explaining that "PTA is designed to compensate for delays by the USPTO," the brief argues that "[i]t is not punitive to decline to grant PTA for delays that are not due to a failure on the part of the USPTO," and therefore concludes that "[g]iving PTA for '[t]his applicant-caused delay is incompatible with the concept of B-delay PTA, which is fundamentally anchored to PTO-caused delay.'"

Webinar on AIA and Patent Prosecution

Strafford will be offering a webinar/teleconference entitled "AIA and Patent Prosecution: Navigating the Ethical Grey Areas" on July 24, 2013 from 1:00 to 2:30 pm (EDT).  Mercedes K. Meyer of Drinker Biddle & Reath, and Patent Docs author Dr. Kevin E. Noonan of McDonnell Boehnen Hulbert & Berghoff will provide guidance on the legal ethics implications of the new patent system and recent changes in patent law, and offer best practices for staying on the right side of the ethical line in patent prosecution.  The webinar will review the following questions:

• How has the AIA changed the ethical landscape for patent attorneys?
• What are the legal ethics implications of supplemental examination?
• What steps should patent counsel take to ensure compliance with legal ethics requirements?

The registration fee for the webinar is $297 ($362 for registration and CLE processing).  Those interested in registering for the webinar, can do so here.

Webinar on Patent Trolls

McDonnell Boehnen Hulbert & Berghoff LLP will be offering a live webinar entitled "Are We Innovators, or Are We Trolls: The Slippery Slope of Defining A Patent Troll" on July 30, 2013 from 10:00 am to 11:15 am (CT).  MBHB attorneys Alison J. Baldwin and Sarah J. Duda will cover proposed governmental anti-patent troll actions and initiatives from both the White House and Congress.  Topics to be covered include:

• An overview of proposed changes including legislative and executive proposals
• How the proposed changes impact whether different business organizations are considered patent trolls
• Whether your organization may be a patent troll under the proposed changes
• Effects on organizations falling under the proposed changes

While there is no fee to participate, attendees must register in advance.  Those wishing to register can do so here.  CLE credit is pending for the states of California, Georgia, Illinois, North Carolina, New Jersey, New York and Virginia.