• Proofread your claims before you sue!

    By Michael Greenfield —

    Federal Circuit SealEven obvious clerical errors in patent claims can doom your lawsuit if not corrected before suit is filed.  This was evident in H-W Technology, L.C. v. Overstock.com, Inc., issued July 11, 2014, where the Federal Circuit upheld the District Court's judgment in favor of defendant Overstock.com because one of H-W's asserted claims contained a clerical error introduced by the PTO.

    And if you were ever wondering whether it might be a good idea to include a pure method limitation in an apparatus claim, the second part of this case makes clear that it is not.

    H-W had brought suit against Overstock for infringement of claims 9 and 17 of its 7,525,955 patent.  Several months into the litigation, Overstock informed H-W that claim 9 as issued was missing a limitation.  The error was obvious from the prosecution history and was simply due to what appears to have been a PTO printing error:  the examiner had allowed the claim containing the limitation but the limitation was missing from the issued patent.  Overstock sought and obtained a certificate of correction several months after being informed of the error but did not move to amend its complaint to reflect the correction.

    Despite the obvious nature of the error and its immediate correction, the Federal Circuit held that the District Court was powerless to correct the error and, therefore, uncorrected claim 9, which was asserted, was unenforceable.  In reaching this conclusion, the Federal Circuit noted that a district court can correct a patent only if, among other things, "the error is evident from the face of the patent."  Perhaps unfortunately for H-W, the claim was logical and intelligible even without the missing limitation (which appears to have been an optional limitation), and nothing in the claims or specification mandated that the missing limitation necessarily be present.

    The Federal Circuit also held that H-W's procurement of a certificate of correction subsequent to filing suit was unavailing.  The Court cited 35 USC § 254, the relevant part of which reads:

    Every such patent [i.e., one for which a certificate of correction has been obtained], together with such certificate, shall have the same effect and operation in law on the trial of actions for causes thereafter arising as if the same had been originally issued in such correct form.

    The Court noted that the express language of the statute limits the effect of the certificate of correction to causes of action arising after the certificate's issuance.  So, even though the error and its correction were obvious to both parties (such being the general nature of errors correctable by a certificate of correction), the statutory language nevertheless requires correction before suit is brought.

    And, so, the error in the claim not being evident from the face of the patent, the courts being powerless to correct the claim, and the certificate of correction being ineffective to cure the claim error after suit was filed, the panel held that uncorrected claim 9 was, in essence, unenforceable.  To hold otherwise, the Court said, "would potentially permit patentees to assert claims that they never asked for not rightly attained.  Such a result would be inequitable and undermine the notice function of patents."

    But the Court noted that corrected claim 9 had not been litigated and, therefore, had not been held invalid (and, consequently, reversed the lower court's ruling to that effect).

    And if you were ever wondering whether it is a good idea to mix method limitations in an apparatus claim, be assured it is not.  In another semi-interesting bonus holding, the Court found H-W's claim 17 invalid as indefinite because it included method limitations in an apparatus claim.  The claim was directed to "a tangible computer readable medium encoded with a computer program for performing contextual searches on an Internet Phone (IP) phone comprising the steps of . . . ," and recited several steps that the computer program conducted (e.g., receiving search criteria from a user, transmitting the criteria to a server, and receiving a list of merchants matching the criteria).  But included among the steps encoded on the medium were two method limitations:

    • "wherein said user completes a transaction with at least one of said merchants . . . ," and

    • "wherein said user selects one of said variety of offers . . . ."

    The District Court held that the claim was indefinite for combining two statutory classes of invention.  The Federal Circuit affirmed, reasoning that it is unclear when infringement occurs in such a claim.

    H-W Technology, L.C. v. Overstock.com, Inc. (Fed. Cir. 2014)
    Panel:  Chief Judge Prost and Circuit Judge O'Malley (former Circuit Judge Rader did not participate in the decision)
    Opinion by Chief Judge Prost

  •         By Sherri Oslick —

    Gavel About Court Report:  Each week we will report briefly on recently filed biotech and pharma cases.

    Aptalis Pharmatech Inc. et al. v. Apotex Inc. et al.
    1:14-cv-01038; filed August 11, 2014 in the District Court of Delaware

    • Plaintiffs:  Aptalis Pharmatech Inc.; Ivax International GmbH
    • Defendants:  Apotex Inc.; Apotex Corp.

    Infringement of U.S. Patent Nos. 7,790,199 ("Modified Release Dosage Forms of Skeletal Muscle Relaxants," issued September 7, 2010) and 7,829,121 (same title, issued November 9, 2010), licensed to Ivax, following a Paragraph IV certification as part of Apotex's filing of an ANDA to manufacture a generic version of Cephalon's Amrix® (cyclobenzaprine hydrochloride, used for relief of muscle spasm associated with acute, painful musculoskeletal conditions).  View the complaint here.

    Pfizer Inc. et al. v. Intellipharmaceutics International Inc. et al.
    1:14-cv-06373; filed August 11, 2014 in the Southern District of New York

    • Plaintiffs:  Pfizer Inc.; Wyeth LLC; Wyeth Pharmaceuticals Inc.; PF Prism C.V.
    • Defendants:  Intellipharmaceutics International Inc.; Intellipharmaceutics Corp.; Intellipharmaceutics Ltd.

    Pfizer Inc. et al. v. Intellipharmaceutics International Inc. et al.
    1:14-cv-01028; filed August 8, 2014 in the District Court of Delaware

    • Plaintiffs:  Pfizer Inc.; Wyeth LLC; Wyeth Pharmaceuticals Inc.; PF Prism C.V.
    • Defendants:  Intellipharmaceutics International Inc.; Intellipharmaceutics Corp.; Intellipharmaceutics Ltd.

    The complaints in these cases are substantially identical.  Infringement of U.S. Patent Nos. 6,673,838 ("Succinate Salt of O-Desmethyl-Venlafaxine," issued January 6, 2004) and 8,269,040 ("Derivatives of Venlafaxine and Methods of Preparing and Using the Same," issued September 18, 2012) following a Paragraph IV certification as part of Intellipharmaceutics' filing of an ANDA to manufacture a generic version of Pfizer's Pristiq® (desvenlafaxine, used to treat depression).  View the Delaware complaint here.

    Senju Pharmaceutical Co., Ltd. et al. v. Metrics, Inc. et al.
    4:14-cv-00141; filed August 8, 2014 in the Eastern District of North Carolina

    • Plaintiffs:  Senju Pharmaceutical Co., Ltd.; Bausch & Lomb, Inc.; Bausch & Lomb Pharma Holdings Corp.
    • Defendants:  Metrics, Inc.; Coastal Pharmaceuticals, Inc.; Mayne Pharma Group Ltd.; Mayne Pharma (USA), Inc.

    Senju Pharmaceutical Co., Ltd. et al. v. Metrics, Inc. et al.
    1:14-cv-04964; filed August 7, 2014 in the District Court of New Jersey

    • Plaintiffs:  Senju Pharmaceutical Co., Ltd.; Bausch & Lomb, Inc.; Bausch & Lomb Pharma Holdings Corp.
    • Defendants:  Metrics, Inc.; Coastal Pharmaceuticals, Inc.; Mayne Pharma Group Ltd.; Mayne Pharma (USA), Inc.

    The complaints in these cases are substantially identical.  Infringement of U.S. Patent Nos. 8,129,431 ("Aqueous Liquid Preparation Containing 2-amino-3-(4-bromobenzoyl)phenylacetic acid," issued March 6, 2012), 8,669,290 (same title, issued March 1, 2014), and 8,754,131 (same title, issued June 17, 2014) following a Paragraph IV certification as part of Metrics' filing of an ANDA to manufacture a generic version of B&L's Prolensa® (bromfenac ophthalmic solution, used to treat postoperative inflammation and reduction of ocular pain in patients who have undergone cataract surgery).  View the New Jersey complaint here.

    Merck Sharp & Dohme Corp. v. Fresenius Kabi USA LLC
    1:14-cv-01018; filed August 7, 2014 in the District Court of Delaware

    Merck Sharp & Dohme Corp. v. Fresenius Kabi USA, LLC
    2:14-cv-04989; filed August 7, 2014 in the District Court of New Jersey

    The complaints in these cases are substantially identical.  Infringement of U.S. Patent Nos. 5,514,650 ("Aza Cyclohexapeptide Compounds," issued May 7, 1996) and 5,952,300 ("Antifungal Compositions," issued September 14, 1999) following a Paragraph IV certification as part of Fesenius' filing of an NDA (under § 505(b)(2) of the Food, Drug and Cosmetic Act) to manufacture a generic version of Merck's Cancidas® (caspofungin acetate, used to treat presumed fungal infections in febrile, neutropenic patients, candidemia and certain Candida infections, esophageal candidiasis, and invasive aspergillosis in patients who are refractory to or intolerant of other therapies).  View the New Jersey complaint here.

    Prometheus Laboratories Inc. v. Par Pharmaceutical Companies Inc. et al.
    1:14-cv-01017; filed August 6, 2014 in the District Court of Delaware

    • Plaintiff:  Prometheus Laboratories Inc.
    • Defendants:  Par Pharmaceutical Companies Inc.; Par Pharmaceutical Inc.

    Infringement of U.S. Patent No. 6,284,770 ("Medicaments for the Treatment of Non-Constipated Female Irritable Bowel Syndrome," issued September 4, 2001) following a Paragraph IV certification as part of Par's filing of an ANDA to manufacture a generic version of Prometheus' Lotronex® (alosetron hydrochloride, used to treat women with severe diarrhea-predominant irritable bowel syndrome).  View the complaint here.

    Esoterix Genetic Laboratories, LLC v. Qiagen N.V. et al.
    1:14-cv-13228; filed August 5, 2014 in the District Court of Massachusetts

    • Plaintiff:  Esoterix Genetic Laboratories, LLC
    • Defendants:  Qiagen N.V.; Qiagen GmbH; Qiagen North American Holdings, Ltd.; Qiagen Manchester, Ltd.; Qiagen, Inc.

    Infringement of U.S. Patent No. 7,294,468 ("Method to Determine Responsiveness of Cancer to Epidermal Growth Factor Receptor Targeting Treatments," issued November 13, 2007) based on Qiagen's offer for sale and sale of test kits allegedly falling outside the scope of an existing licensing agreement.  Also, various claims sounding in state law.  View the complaint here.

    Hospira Inc. et al. v. Ben Venue Laboratories Inc. et al.
    1:14-cv-01008; filed August 1, 2014 in the District Court of Delaware

    • Plaintiffs:  Hospira Inc.; Orion Corp.
    • Defendants:  Ben Venue Laboratories Inc.; Hikma Pharmaceuticals PLC; West-Ward Pharmaceuticals Corp.

    Infringement of U.S. Patent No. 6,716,867 ("Use of Dexmedetomidine for ICU Sedation," issued April 6, 2004) following a Paragraph IV certification as part of Ben Venue's filing of an ANDA to manufacture a generic version of Hospira's Precedex® (dexmedetomidine hydrochloride injection, used for the sedation of initially intubated and mechanically ventilated patients during treatment in an intensive care setting).  View the complaint here.

    Mallinckrodt LLC et al. v. Zydus Pharmaceuticals (USA) Inc.
    1:14-cv-04901; filed August 1, 2014 in the District Court of New Jersey

    • Plaintiffs:  Mallinckrodt LLC; Mallinckrodt Inc.; Nuvo Research Inc.
    • Defendant:  Zydus Pharmaceuticals (USA) Inc.

    Infringement of U.S. Patent Nos. 8,217,078 ("Treatment of Pain with Topical Diclofenac," issued July 10, 2012), 8,546,450 (same title, issued October 1, 2013), 8,618,164 (same title, issued December 31, 2013), and 8,741,956 (same title, issued June 3, 2014) following a Paragraph IV certification as part of Zydus' filing of an ANDA to manufacture a generic version of Mallinckrodt's Pennsaid® (diclofenac sodium topical solution, used for the treatment of signs and symptoms of osteoarthritis of the knee(s)).  View the complaint here.

  • CalendarAugust 27-28, 2014 – "Global Patent Prosecution: Comparing Europe, China, and U.S. Law & Practice" (Intellectual Property Owners Association) – 12:00 to 1:00 pm (ET)

    August 28, 2014 – "Alice Corp. vs. CLS Bank: What’s Eligible, What’s Not, and What’s Still to be Determined?" (Technology Transfer Tactics) – 1:00 to 2:00 pm (ET)

    September 4, 2014 – "Patents and Export Control Compliance: Managing Risk and Avoiding Unintentional Violations — Minimizing Export Control Liability in Patent Application Preparation, Development and Analysis of Innovation, and Licensing" (Strafford) – 1:00 to 2:30 pm (EDT)

    September 7-9, 2014 – 42nd Annual Meeting (Intellectual Property Owners Association) – Vancouver, Canada

    September 11, 2014 – "Post-AIA Section 102 and Prior Art: Navigating the Expanded Scope of Prior Art and AIA Exceptions" (Strafford) – 1:00 to 2:30 pm (EDT)

    September 11-12, 2014 - Advanced Patent Prosecution Workshop 2014: Claim Drafting & Amendment Writing (Practising Law Institute) – Chicago, IL

    September 16, 2014 – "Section 103 and Obviousness: Capitalizing on CCPA and Early Federal Circuit Precedent — Strategies for Withstanding Obviousness Rejections and Attacks on Patent Validity and Patentability" (Strafford) – 1:00 to 2:30 pm (EDT)

    September 18-19, 2014 – FDA Boot Camp (American Conference Institute) – Boston, MA

    September 30, 2014 – 2014 Intellectual Property Continuing Legal Education Seminar (DuPont and Widener University School of Law) – Wilmington, DE

    September 30 – October 1, 2014 – Paragraph IV Disputes Master Symposium (American Conference Institute) – Chicago, IL

    October 2, 2014 – "USPTO Guidance for Determining Subject Matter Eligibility In View of U.S. Supreme Court's Mayo and Myriad Decisions" (McDonnell Boehnen Hulbert & Berghoff LLP) – 10:00 to 11:15 am (CT)

    October 2, 2014 – "Conflicts in Patent Prosecution: Minimizing Risks of Malpractice Liability and Ethics Sanctions" (Strafford) – 1:00 to 2:30 pm (EDT)

    October 29-30, 2014 - Congress on PIV Litigation (Momentum) – Philadelphia, PA

    ***Patent Docs is a media partner of this conference or CLE

  • IPO #2The Intellectual Property Owners Association (IPO) will offer two one-hour webinars on "Global Patent Prosecution: Comparing Europe, China, and U.S. Law & Practice" on August 27 & 28, 2014 beginning at 12:00 pm (ET) each day.  The first day will feature Philip L. Cupitt, Ph.D of Finnegan, Henderson, Farabow, Garrett & Dunner, LLP; Samson Helfgott of Katten Munchin Rosenman LLP; and Deshan Li, Ph.D. of Unitalen, and the second day will feature Ji Liu of CCPIT Patent and Trademark Law Office; Martin D. Hyden of Finnegan, Henderson, Farabow, Garrett & Dunner, LLP; and Samson Helfgott of Katten Munchin Rosenman LLP.  Panelists will compare and contrast patent prosecution law and practice in the three jurisdictions with regard to the key criteria of Obviousness and Written Description.

    The registration fee for the webinar is $130 per webinar (government and academic rates are available upon request).  Those interested in registering for the webinar can do so here.

  • Strafford #1Strafford will be offering a webinar/teleconference entitled "Conflicts in Patent Prosecution: Minimizing Risks of Malpractice Liability and Ethics Sanctions" on October 2, 2014 from 1:00 to 2:30 pm (EDT).  The webinar will provide guidance to IP counsel on the conflicts issues that often arise in patent prosecutions, and outline best practices to identify and address the risks — and to minimize conflicts that can lead to malpractice liability and ethical violations.  The webinar will review the following questions:

    • What policies and practices should counsel have in place to identify potential conflicts in patent prosecutions?
    • What steps can patent prosecutors take to minimize the risk of subject matter conflicts?
    • How should patent counsel respond after identifying conflicts?

    The registration fee for the webinar is $297 ($362 for registration and CLE processing).  Those registering by September 5, 2014 will receive a $50 discount.  Those interested in registering for the webinar, can do so here.

  • Independence HallMomentum will be holding its 2nd Congress on PIV Litigation on October 29-30, 2014 in Philadelphia, PA.  The conference will offer presentations on the following topics:

    • Key Takeaways for Brand and Generic Drug Manufacturers from Recent Case Law

    • Are Your Ducks in a Row? — Examining the Top 3 Pre-Suit Due Diligence Issues Counsel on Both Sides Should Be Evaluating In Anticipation of a Paragraph IV Suit

    • The Expansion of the Hatch Waxman Safe Harbor — Addressing HOW Recent Developments in the Evolution of Case Law Are Impacting Litigation Approaches to Paragraph IV Disputes

    • PTO v. Federal District Court — Evaluating the Emerging Impact of Parallel PTO Proceedings on the Procedural Dynamics of Hatch Waxman Litigation

    • Patent Reform — What You Don't Know is In There — A True Examination of Proposed Patent Legislation and the Impact Each Bill Could Have on the Pharmaceutical Industry and Related IP Litigation

    • Insider Tips for Obtaining Successful Results When Engaged in a Paragraph IV Dispute in the District of Delaware — Proven Strategies for Effectively Engaging with the Bench and Working with Local Counsel

    • Insider Tips from the Bench on How to Most Effectively Present Experts and Witness during Paragraph IV Litigation

    • Forfeiture and Multiple Filers — Forfeiture and Multiple Filers: Insights for Avoiding or Triggering Forfeiture Events in Hatch-Waxman Litigation Involving Multiple ANDA Filers

    • Spotlight Address — Perspectives from the FTC on Pay-for-Delay Settlements

    • Paragraph IV Settlements Post-Actavis — Can They Be Done and If So, How? — Live Mock Negotiation

    • Communication with Key Stakeholders — Litigation Communication Strategies for In-House Counsel When Actively Engaged in a Paragraph IV Dispute

    • When Prior Settlements Come Back To Haunt You — What Brand Name and Generic Drug Manufacturers Can Learn from Recent Third Party Payor Suits Challenging the Implications of Hatch Waxman Litigation on Drug Competition

    In addition, two interactive working group sessions will be offered during the conference.  The first workshop is entitled "PTEs, Combination Products and 'Product Hopping': Life Cycle Management Insights for Brand Name Drug Manufacturers Engaged in Paragraph IV Litigation," and the second is entitled "At Risk Launches: An Examination of the Business Benefits and Legal Risks of Launching at Risk — How to Determine If It’s Truly Worth It . . . or Not Making the decision to launch a product 'at risk' is one that can bring with it great financial."

    MomentumThe agenda for the International Congress on Paragraph IV Litigation can be found here.

    The registration fee for the conference is $1,395 (in-house/corporate), $1,795 (private practice), or $1,95 (all other companies).  Those interested in registering for the conference can do so here.

    Patent Docs is a media partner of Momentum's Congress on PIV Litigation.

    Photograph of Independence Hall (above) by Dan Smith, from the  Wikipedia Commons under the Creative Commons license.

  • Strafford #1Strafford will be offering a webinar/teleconference entitled "Patents and Export Control Compliance: Managing Risk and Avoiding Unintentional Violations — Minimizing Export Control Liability in Patent Application Preparation, Development and Analysis of Innovation, and Licensing" on September 4, 2014 from 1:00 to 2:30 pm (EDT).  The webinar will provide guidance for patent counsel on navigating the intersection of patents and export control laws, examine the challenges facing patent owners, when and where export control issues arise, and licensing issues, and offer best practices for complying with export control laws.  The webinar will review the following questions:

    • What export control compliance challenges do patent owners and applicants face?
    • When do export violations arise in the patent context?
    • What are the best practices for counsel to patent owners for compliance with ITAR and EAR 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.

  • By Donald Zuhn —

    On March 4, the U.S. Patent and Trademark Office issued a guidance memorandum, entitled "Guidance For Determining Subject Matter Eligibility Of Claims Reciting Or Involving Laws of Nature, Natural Phenomena, & Natural Products" (or "Myriad-Mayo Guidance"), to implement a new procedure for determining the subject matter eligibility of claims under 35 U.S.C. § 101 in view of the Supreme Court's decisions in Association for Molecular Pathology v. Myriad Genetics, Inc. (2013), and Mayo Collaborative Services v. Prometheus Laboratories, Inc. (2012).  At a biotechnology/chemical/pharmaceutical (BCP) customer partnership meeting in April, the Office announced that it would be hosting a public forum on the Guidance in May to receive public feedback on the Guidance, and at that forum encouraged shareholders to submit written comments on the Guidance.  The original "end of June" deadline for submitting comments on the Guidance was subsequently extended to July 31.  With that extended deadline now passed, Patent Docs has summarizing selected comments in a series of posts.

    AUTMThe Office has posted the comments that were submitted on the USPTO website.  The comments are divided into five groups (with the number of submissions in each group also provided):  Intellectual property organizations and other associations (18), academic and research institutions (7), law firms (6), companies (9), and individuals (42).  Today, we examine the comments submitted by the Association of University Technology Managers (AUTM), Council on Governmental Relations (COGR), Association of American Universities (AAU), and Association of Public and Land-Grant Universities (APLU).

    COGRThe comments letter submitted by the four academic groups begins by noting that AUTM is a nonprofit organization with more than 3,000 members from more than 300 universities, research institutions, and teaching hospitals as well as numerous businesses and government organizations; COGR is an association of 190 U.S. research universities and their affiliated academic medical centers and research institutes; AAU is an association of 60 U.S. and two Canadian research universities; and APLU is a research, policy, and advocacy organization representing 234 public research universities, land-grant institutions, state university systems, and affiliated organizations.  The comments letter indicates that "[t]he majority of AUTM members and the entire COGR, AAU and APLU memberships represent nonprofit research institutions that do not directly commercialize their discoveries and intellectual property but are dependent on the private sector to invest in, develop and market products and services based on university-created technology."  According to the four academic organizations, "[w]ith over $36 billion in net sales of products based on inventions made at institutions represented by our associations, it has been estimated that academic technology transfer generates $80 billion dollars in economic activity annually in the U.S."

    AAUAfter describing the contribution of the organizations' members to the economy and innovation in the U.S., the groups state that they are "deeply concerned about the PTO Guidance Memorandum and its unwarranted, as well as legally inconsistent broad changes in examination practice."  In particular, the letter asserts that "[t]he Guidance adversely and unnecessarily impacts our ability not only to license and commercialize future discoveries and inventions, but also the validity of many existing patents for products, particularly in life science areas which make up the majority of university patents."

    APLUThe academic organizations identify one primary concern and two major flaws with the Guidance.  With respect to the former, the groups suggest that "the Guidance is overly broad and contravenes the Supreme Court's own warning in Mayo against over-interpreting its holdings in a way that might stifle innovation, the very kinds of innovation to which U.S. universities contribute," and support opponents of the Guidance "who have criticized the emphasis on structure rather than the functional characteristics of a product."  As for the major flaws, the groups argue that the Guidance provides "[a]n inappropriate and legally questionable interpretation of Myriad," and as a result "[t]o patent a product (e.g., a drug) purified from a natural source under the new Guidance, the claimed product must be both structurally and functionally different from its natural state, a position not supported by case law."  The letter contends that "earlier cases emphasized functionality rather than the need for a significant modification from their natural form."

    The letter indicates that the second flaw is the Guidance's "[m]isinterpretation of Mayo [that] could seriously harm the diagnostics industry and patients relying on its products."  According to the academic organizations, "[t]he examples provided in the Guidance [relating to diagnostic methods] are unclear, ambiguous, and raise more questions than they answer."

    The letter argues that "[b]y drafting and releasing this Guidance, the PTO is assuming a judicial authority that is not properly PTO's to assume by erroneously re-interpreting Supreme Court case law, with no opportunity for public comment."  The comments letter concludes by stating that:

    Numerous AUTM, COGR, AAU, and APLU members . . . find the Guidance unsettling because it could improperly prevent universities from patenting valuable and potentially life-saving technology and effectively block these technologies from ever reaching the public.  It could also create grave uncertainty about pending and issued university patents and remove the incentive for companies to license them and create innovative products and services that will benefit society.

    The groups urge the USPTO revise the Guidance, arguing that "[f]ailing to do so will eviscerate the benefits of that research by unnecessarily denying patent protection to promising technologies, stifle innovation in academia, seriously harm the ability of companies to develop products that will help the American public, and significantly, adversely impact job growth in America."

    Patent Docs will examine other Guidance comments in subsequent posts.

    For additional information regarding this topic, please see:

    • "Examination of Myriad-Mayo Guidance Comments — International Bioindustry Associations," August 11, 2014
    • "Examination of Myriad-Mayo Guidance Comments — ACLU," August 5, 2014
    • "Guest Post: Overview of First Published Comments on Myriad-Mayo Patent Eligibility Guidance," July 13, 2014
    • "Guest Post: USPTO Public Forum on Patent Guidance: My Thoughts as a Speaker and Attendee," June 11, 2014
    • "USPTO Holds Forum on Subject Matter Eligibility — Part IV," May 22, 2014
    • "USPTO Holds Forum on Subject Matter Eligibility — Part III," May 15, 2014
    • "USPTO Holds Forum on Subject Matter Eligibility — Part II," May 14, 2014
    • "Guest Post: How to Patent Grapefruit Juice — The New USPTO Guidance for Patent Eligible Subject Matter Is Both Sticky and Sour," May 13, 2014
    • "USPTO Holds Forum on Subject Matter Eligibility — Part I," May 12, 2014
    • "USPTO Tries to Address Public Misunderstandings Regarding Myriad-Mayo Guidance," April 16, 2014
    • "USPTO Issues Guidance for Analyzing Subject Matter Eligibility of Claims Reciting Laws of Nature/Natural Principles, Natural Phenomena or Natural Products," March 4, 2014

  • By Kevin E. Noonan —

    NIHOn Monday, Genetic Engineering and Biotechnology News (GEN) published a list of the Top 50 NIH-funded U.S. universities in fiscal year October 1st – September 30th.  Geographically, California leads the list of most Federal research monies going to schools in the state.  The list, set forth below, shows that private universities represent 22 of the 50 universities and garner about 24% of the funding (disproportionately, with Johns Hopkins University, Duke, Yale, Stanford, Washington and the Universities of Pittsburgh and Pennsylvania getting more thanm 50% of the total of almost $19 billion in NIH funding).

    Table*Private universities

    The top 50 get about 80% of the total awarded, representing "almost 50,000 competitive grants given to more than 2,500 universities, medical schools and other research institutions" at home and abroad according to GEN.  The leader, Johns Hopkins, received almost one thousand awards in 2014, while the majority of the rest of the schools received between 300-500 awards.

    Source (according to GEN): Source: NIH Awards by Location and Organization, database contained within NIH Research Portfolio Online Reporting Tools (RePORT) website, Fiscal Year 2014, last updated by NIH on August 11

  • By Kevin E. Noonan —

    000_0149 2Earlier this month, an international effort* led by Stephen J. O'Brien at the Oceanographic Center, Nova Southeastern University, Ft. Lauderdale, Florida reported the complete genomic sequencing of the domestic cat, Felix catus.  The report, entitled "Annotated features of domestic cat – Felis catus genome," was published in GigaScience 2014, 3:13 (August 5, 2014).

    The study reports sequencing of a female Abyssinian cat named Cinnamon, a mixed-breed cat from Russian named Boris, and Sylvester, a wildcat ancestor of domestic cats.  Most significantly, the report showed that domestic cats have retained "a highly conserved ancestral mammal genome organization" in comparison with ancestral cats (see Driscoll et al., 2007, "The near eastern origin of cat domestication," Science 317: 519–23).  Both species, F. catus and Felix silvestris silvestris, have 38 chromosomes, 18 pairs of autosomes, and two pairs of dimorphic gender-determining chromosomes.

    The report is replete with arcane details of the cat genome, including the discovery of:

    • 217 loci of endogenous retrovirus-like elements (amounting to 55.7% of the entire genome, comprised of long interspersed elements (LINEs), short interspersed elements (SINEs), satellite DNA, retroviral long terminal repeats (LTRs) and "others");

    • 21,865 protein coding genes (open reading frames or ORFs), detected by comparison with eight mammalian genomes (from human, chimpanzee, macaque, dog, cow, horse, rat, and mouse);

    • 99,494 "new" single nucleotide polymorphisms (SNPs), in addition to 3,078,438 previously identified SNPs;

    • 8,355 new insertion/deletion events (indels);

    • 743,326 evolutionarily constrained elements (ECEs);

    • 3,182 microRNA homologues;

    • 25 novel families of complex tandem repeat elements;

    • 53,710 short terminal repeat (STR) loci;

    as well as 176 kb of mitochondrially derived DNA and 125 kb of partial feline retrovirus-derived DNA.  In addition, 10.5% of cytosine residues are methylated in the cat genome.

    There was also extensive evidence of regions of "recent" autosomal segmental duplications.  Specifically:

    Among all variants 24.6% (693,428 SNVs and 122,333 indels) were heterozygous in Felis silvestris.  Between the genomes of Felis catus and Felis silvestris some 2.9 million (2,847,548) single nucleotide variants and ∼1.9 Mbp of insertions and deletions were detected.  Observed differences were significantly fewer compared to difference between human and chimpanzee genomes (~35 million SNV and ~90 Mbp of indels).

    The report also contains extensive comparison between domestic cats and other species ("reference genomes") in terms of gene numbers, using genes with the longest the longest mRNA and corresponding coding sequences (click on table to expand).

    Table
    The intriguing finding that modern domestic cats are more similar to their wildcat forebears than are dogs to wolves (or humans and chimpanzees, for all the touted 98% similarity between simian and human genomes) is not explained in the report.  Regarding dogs, comparison of breed types provides some hints:  while there are about 41 breeds of domestic cat, there are 339 breeds of dogs, sorted into 10 groups (terriers, retrievers, pointer/setters, hounds, companion or "toy" dogs, "herding" dogs like sheepdogs, mastiffs, non-sporting dogs like Dalmatians and bulldogs, sporting dogs like spaniels, and working dogs like the Akita and Alaskan Husky).  These dogs vary in overall size, leg length, muzzle shape, fur length and density, muscularity, and temperament, among other attributes.  Many of the features of these dog breeds have been selected by human breeding practices for traits and features having at least some genetic component.  In addition, the process of domesticating a dog from its wolf ancestors involved changing its personality from human predator to human companion and allowed the dog to permit humans to take the "alpha" role of pack leader.

    Cats, on the other hand do not vary that much in size and in fact show most of their variation in coat and eye color and coat pattern.  There also have been many fewer behavioral changes in domestic cats than in dogs, as evidenced by cats' (in)famous independence.  While these are merely speculations, it seems likely that the domestication process required far fewer genetic adaptations in cats than it seems were required in dogs, and thus their modern genomes retain much closer similarity to the ancestral European wild cat than do dogs to their wolfish ancestors.

    Finally, for the cognoscenti (and those with a low sense of humor), the authors also report their development of a cat genome browser, designated Genome Annotation Resource Field or GARField (groan).

    * Other members of the team included scientists from the Theodius Dobzhansky Center for Genomic Bioinformatics, St. Petersburg State University, St. Petersburg RU (Gaik Tamazian, Serguei Simonov, Pavel Dobrynin, Alexey Makunin, Anton Logachev, Aleksey Komissarov, Andrey Shevchenko, Vladimir Brukhin, Nikolay Cherkasoy, Anton Svitin, Klaus-Peter Koepfli, and Joan Pontius); Laboratory of Neurogenetics, NIAAA, Rockville, MD USA (Carlos A Driscoll, Kevin Blackstone, Cristina Barr and David Goldman); CIIMAR – Interdisciplinary Center of Marine and Environmental Research, University of Porto, Porto PT (Agostinho Antunes); Department of Animal and Food Science, Veterinary Molecular Genetics Service, Universitat Autonoma de Barcelona, Barcelona ES (Javier Quilez);  IBE, Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIS, PRBB, Barcelona ES (Belen Lorente-Galdos and Tomas Marques-Bonet); Department of Computer Engineering, Bilkent Univesity, Ankara TK (Can Alkan); Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research, Frederick MD USA (Marylin Menotti-Raymond and Victor David); and the Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia MO (Krsitina Narfstrom).

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

    • "Leg Length Variation in Dogs and its Relevance to Human Mutations," August 31, 2009
    • "The Genetic Basis of Coat Variation in Dogs," August 30, 2009
    • "From Toy Poodle to Rottweiler: Why Is Fido So Small (or Large)?" April 9, 2007