Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: Paul Gilbert Cole

By Kevin E. Noonan --

Earlier this summer, in Ariosa Diagnostics, Inc. v. Sequenom, Inc., the Federal Circuit affirmed a decision by the District Court for the Northern District of California granting summary judgment of invalidity of the asserted claims of U.S. Patent No. 6,258,540 (see "Ariosa Diagnostics, Inc. v. Sequenom, Inc. (Fed. Cir. 2015)").  Last month, Sequenom filed a petition for rehearing en banc, arguing that the panel's decision in June was inconsistent with the Supreme Court's decisions in Diamond v. Diehr, 450 U.S. 175 (1981), Mayo v. Prometheus Laboratories, 132 S. Ct. 1289 (2012), and Association for Molecular Pathology v. Myriad Genetics, 133 S. Ct. 2107 (2013), and that the panel's decision poses a threat to patent protection in multiple fields of invention.  On August 27, twelve amicus curiae briefs were filed in support of Sequenom's petition for rehearing en banc.  Over the next few weeks, Patent Docs will examine these amicus briefs.  Today, we review the brief submitted by Paul Gilbert Cole (at right).

In the brief's Statement of Interest, the amicus states that he is "a practising UK and European patent attorney, is a visiting professor in IP Law at Bournemouth University in the UK and has been writing about and teaching patent law for over 35 years."  He is "concerned with the integrity of the legal system and the correctness of the consequential guidance that is given to patent examiners in the USPTO" and in his professional opinion "the panel decision's application of § 101 exceeds the scope of the Supreme Court's § 101 jurisprudence and the scope of Article 27 of the TRIPS agreement."

Mr. Cole makes several arguments.  First, he contends that the panel decision is contrary to controlling Supreme Court and other precedent, citing a dozen cases ranging from Mayo and Myriad to Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95 (C.C.S.D.N.Y. 1911), and Merck & Co. v. Olin Mathieson Chem. Corp., 253 F.2d 156 (4th Cir. 1958).  He also argues that it is "based on a legally incomplete and a legally and factually incorrect interpretation of the invention described and claimed in U.S. Patent No. 6,258,540."  The brief then sets forth three "precedent-setting questions of exceptional importance":

(1) Should the context in which a claimed method that involves a newly discovered natural phenomenon be disregarded for the second part of the test in Mayo, so that steps that are known but only in different contexts do not count towards eligibility?
(2) How relevant to the natural phenomenon exclusion of § 101 is a new and beneficial result never attained before and evidencing inventive step under § 103?
(3) Is the second part of the Mayo test applied in the breadth of the Panel Opinion incompatible with the obligations of the United States under Article 27 of TRIPS?

The brief then sets forth Mr. Cole's reasons for urging the court to grant Sequenom's en banc petition.

The first reason Mr. Cole asserts is that the decision will "likely" be the basis of further guidance from the U.S. Patent and Trademark Office.  This is problematic, according to Mr. Cole, because the Office "has a history of over-broad interpretation of Supreme Court and other decisions, which has created widespread difficulty for patent applicants and hence widespread adverse comment from both individuals and organizations."  This tendency should not be encouraged.

Second, Mr. Cole asserts that the District Court and the panel "mischaracterized" the amplified cffDNA as being a natural phenomenon, when instead it should be considered as a manufacture and hence to fall within an expressly recited patent-eligible category of invention according to the statute.  (It could be argued that this rationale underlay the Supreme Court's distinction between patent-ineligible genomic DNA and patent-eligible cDNA in its Myriad decision).  In addition, Mr. Cole argues that the amplification primers are not natural phenomena, because they do not exist in the bloodstream; he further states that "[t]he fact pattern here diverges materially from that in Myriad where neither wild-type BRCA1 nor the corresponding cDNA were reported as having been isolated as real and tangible molecules" (based on the lack of description of actually isolating a BRCA cDNA clone, which while true doe not answer the Section 112 issue: the entire coding sequence was disclosed and it was within the skill of the ordinarily skilled artisan to make such a cDNA clone from the information disclosed in Myriad's patents).  Mr. Cole also argues (citing Learned Hand in Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95 (C.C.S.D.N.Y. 1911)) that the real and tangible oligomer sequences in their amplified form have become for every practical purpose a new thing commercially and analytically (wherein the amplified PCR fragments can be detected visually by ethidium bromide staining, something that the unamplified cffDNA cannot be).  The brief also cites Hartranft v. Wiegmann, 121 U.S. 609 (1887), as that case was cited in support of the Court's Diamond v. Chakrabarty decision, wherein "a change of form accompanied by new utility is the hallmark of a manufacture." 447 U.S. 303 (1980).  Along these lines, the brief echoes the Chakrabarty decision in stating that "[t]he amplified sequences are the product of human ingenuity being a non-naturally occurring composition of matter having (following the wording in Chakrabarty and Myriad) a distinctive name (amplified maternal plasma sequences), character (short oligomer sequences in high and analyzable concentration) and use (analytical detectability) not possessed by maternal cffDNA," and hence that the sequences themselves met the eligibility test and thus negated the panel's basis for applying the Mayo/Alice test.

In the brief's third basis for urging en banc reconsideration, Mr. Cole argues that the panel found patent ineligibility based on a consideration of the claim limitations individually and ignored the Court's exhortation that "ordered combinations" can recite patent-eligible subject matter.  Under a proper application of the law, the brief argues that the "starting point" for the claimed methods was maternal plasma or serum (not cffDNA), and thus the selection of this source "set[s] the claimed method apart from the prior art," citing United States v. Adams, 383 U.S. 39 (1966).  Considered as such an ordered combination, the brief maintains that the claims are directed to "a hitherto unavailable test of high sensitivity for a range of medical conditions that can be applied early in pregnancy and avoids the risks to the fetus inherent in amniocentesis and that revolutionized prenatal care," i.e., something that is patent eligible.

Point four of the brief expands on this assessment of Sequenom's claims as reciting "an ordered combination" by applying the rule from Webster Loom Co. v. Higgins, 105 U.S. 580, 591 (1881), that "if a new combination and arrangement of known elements produce a new and beneficial result, never attained before, it is evidence of invention."  Here, according to the brief, "the claimed combination of starting material and method steps here produced a new and beneficial test for fetal abnormalities and the like [that] is affirmative evidence of invention" and the panel erred in not considering this.

Finally, Mr. Cole cites the conflict of the panel's decision with U.S. treaty obligations including the TRIPS agreement, citing a comment from the Japan Intellectual Property Association to the effect that "the U.S. was introducing special eligibility criteria contrary to the international trend of intellectual property protection."  The brief also cites Article 27.1 of the TRIPS agreement, which the brief asserts is binding on member nations and requires patents to be available "for any inventions, whether products or processes, in all fields of technology, provided that they are new, involve an inventive step and are capable of industrial application, and that patent rights should be enjoyable without discrimination as to the field of technology."  And the brief cites Art. 52(2)(a)-(d) for the provisions that define unpatentable subject matter in Europe that are limited to those satisfying these criteria:

If a new property of a known material or article is found out, that is mere discovery and unpatentable because discovery as such has no technical effect and is therefore not an invention within the meaning of Art. 52(1) EPC.  If, however, that property is put to practical use, then this constitutes an invention which may be patentable.  To find a previously unrecognised substance occurring in nature is also mere discovery and therefore unpatentable.  However, if a substance found in nature can be shown to produce a technical effect, it may be patentable...."

The brief closes by accusing the panel decision as being "an internationally discordant, not harmonious, result, contrary to the eligibility requirements of TRIPS Article 27," and notes that the European counterpart was challenged on inventive step not eligibility grounds (and was found to satisfy the EPC requirements).

For additional information regarding this topic, please see:

• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: Bioindustry Association," September 20, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: WARF, Marshfield Clinic, and MCIS, Inc.," September 17, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: BIO and PhRMA," September 16, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: Amarantus Bioscience Holdings, Personalis, Inc., and Population Diagnostics, Inc.," September 15, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: Coalition for 21st Century Medicine," September 14, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: IPO," September 8, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: Professors Lefstin and Menell," September 6, 2015
• "Amicus Briefs in Support of Sequenom's Petition for Rehearing En Banc: 23 Law Professors," September 3, 2015
• "Amici Support Sequenom's Petition for Rehearing En Banc," August 28, 2015
• "Sequenom Requests Rehearing En Banc," August 18, 2015
• "Ariosa Diagnostics, Inc. v. Sequenom, Inc. (Fed. Cir. 2015), June 22, 2015

Comments

[EG]

Paul,

Always appreciate your insights on our patent and court system from across the Pond. As you're likely aware, I don't always agree with them, but please understand that doesn't detract from their value for thoughtful discussion and debate.

What you argue for in your request would do much to help sort out the currently chaotic situation we have here in the States on the patent-eligibility issue under 35 USC 101. Unfortunately for your arguments, as well as the "rule of law," our patent law jurisprudence is currently being dominated by judges and especially Justices of SCOTUS who are making policy judgments which should be reserved to our Congress. In short, we have judicial activism where determinations on patent-eligibility are being made without trying to understand the facts (i.e., the technology being claimed) or the relevant patent statutes (i.e., 35 USC 101) which leads to mind-boggling nonsensical court decisions that are little more than judicial fiat. Wish it were otherwise.

[The Memory Motel]

Paul Cole: "[the Office] has a history of over-broad interpretation of Supreme Court and other decisions, which has created widespread difficulty for patent applicants and hence widespread adverse comment from both individuals and organizations."

Actually the exact opposite is true but Paul Cole isn't exactly the most forthcoming person in the room. Ever.

[The Memory Motel]

EG: "we have judicial activism where determinations on patent-eligibility are being made without trying to understand the facts"

Of course "EG" suffers from a well-documented difficulty in understanding what is a "fact" and what is not a "fact."

Here is a fact: Prometheus stated in open court that its claim covered the steps of (1) obtaining data using an old technique and (2) thinking a "new" thought about that data.

It doesn't take much intelligence to see where a patent system that allows such claims to be granted and enforced is headed. And yet many people -- including EG and many other self-identified "experts" -- have apparently chosen to "not understand" that simple fact for many years.

Now we yet have another case dealing with a class of incredibly broad claims with the potential to dramatically affect the public's rights to fundamental diagnostic facts. Specifically, we have the situation where X uses a well-known detection method to determine a natural fact, and then attempts to monopolize that fact by broadly claiming "A method wherein said method comprises the use of old technology to detecting [insert fact here]."

On an earlier thread dealing with this topic, Paul Cole was asked to directly address the implications of his position reqarding Sequenom's claim and he simply refused to do so. It's safe to assume that Paul Cole either does not understand the facts about Sequenom's claim (and claims like it) or Paul Cole simply does not want to discuss those facts because they make him uncomfortable (can anyone guess why?).

But here's the deal: those facts aren't going away. They didn't go away before Prometheus v. Mayo when the exact same crowd of cheerleaders tried to make the bad facts go away. And they didn't go away when before Myriad when the exact same crowd of cheerleaders tried to make other equally bad facts go away.

Here again is the hypothetical and questions that were asked on the previous thread. Maybe one of the defenders of Sequenom's claim will step up this time and answer them.

Hypothetical:

Biologist uses PCR to identify a new uncultured bacteria that lives in soil. Biologist claims "use PCR to detect [insert name of new species here]".

Question: Is that claim eligible? If so, why? If the claim is eligible, could the claim be made any simpler (i.e., broader?) including specific reference to all additional known methods?

If the claim isn't eligible, why is that the case and how does it differ from Sequenom's claim? What could/should be added to the claim to make it eligible?

[Paul Cole]

Many thanks for your summary. I have one small quibble.

I spent several not so happy days studying the BRCA1 patent which I confess I view with the eyes of a chemist rather than a biotechnologist.

As you rightly say the patent listed the full length cDNA sequence. I did not find an example reporting the actual isolation of the cDNA as a physical molecule, and suspect that the experimental work had not progressed beyond probing various libraries for partial sequences and the computer reconstruction of the complete cDNA sequence from these partial sequences. However, my understanding is that once this stage had been reached the production of physical BRCA1 cDNA was a trivial step, and have learned that this cDNA is now a commercially available product.

The situation regarding wild-type BRCA1 is quite different. The patentees had indeed found the exons and knew both their sequences and their relative positions in the wild-type gene. However, they had sequenced only 27,000 of the 80,000 or so nucleotides in BRCA1, and there were regions listed as vvvvvvvvv which did not impress Judges Moore and Bryson in the Federal Circuit. Isolation of full length BRCA1 as a physical molecule was not reported in the patent, nor did the patent contain detailed directions for doing so.

“Isolated DNA” as construed by Judge Sweet at first instance meant a segment of DNA nucleotides existing free from other cellular components normally associated with native DNA, including proteins and other DNA sequences comprising the remainder of the genome. In their reply brief to the Supreme Court Myriad argued that isolation required separation of the specific DNA of interest from the rest of the DNA in the body and even from the rest of the fragmented DNA that might be present in a test tube outside the body. In their subsequent respondent’s brief Myriad argued that the specific isolated BRCA1 and BRCA2 molecules, once defined, are either separated from surrounding genomic and cellular matter at precise locations chosen by the Myriad inventors or assembled in a laboratory in the case of cDNA.

If Myriad were arguing that their BRCA1 patent described the separation of wild-type BRCA1 at precise locations of their choice, then my understanding is that argument is based on falsehood, which it appears was detected both by Judges Moore and Bryson in the Federal Circuit and by Justice Thomas in the Supreme Court who was well aware of the limitations of what had been disclosed in the patent and alluded to those limitations in his opinion.

The point, in my view, is not a question whether the disclosure of the BRCA1 patent sufficed under 35 USC 112 to support a claim to the wild-type gene (which I suggest is not proven) but whether Myriad's representatives insofar as the disclosure of the patent was concerned were presenting a falsehood to the Court which I think they were. Non-technical judges may not fully understand molecular biology, but they are good at detecting falsehood when they see it and did so here.