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Rules for Patenting Genetic Biomarkers Are Updated in Roche v. CepeidAs the readers of this blog are no doubt aware, patenting DNA defined only by a naturally occurring nucleotide sequence was banned by the U.S. Supreme Court in the landmark case of Association for Molecular Pathology v. Myriad Genetics, Inc. The patentee in that case attempted to patent “isolated” DNA with the natural sequence of the BRCA1 breast cancer gene. The Supreme Court believed this was an attempt to claim the natural gene itself, which it believed to be an ineligible “natural phenomenon.” Prior to this decision, newly discovered DNA sequences could be patented, so long as they were claimed to be “isolated” from their original host organism.

However, the Supreme Court opinion specifically left open the possibility that artificial methods of using natural DNA could still be patented; some of Myriad’s claims were for such methods, and their eligibility for patenting was unchallenged, and thus not directly consider by the court.

The Supreme Court in Myriad also did not consider whether properties of artificial DNA other than its sequence could distinguish it from a natural product. The patentee in Myriad had simply relied on the magic word “isolated” to draw a distinction between its invention and what is natural, and the Supreme Court was not enchanted.

Questions have lingered over to what extent artificial processes using DNA can be patented, and to what extent DNA with a natural sequence but other artificial properties can be patented. The U.S. Court of Appeals answered both questions in the October 9 decision in Roche Molecular Systems, Inc. v. Cepheid.

The invention in Cepheid arose from the discovery of unique genetic biomarkers found in the pathogenic bacterium Mycobacterium tuberculosis. M. tuberculosis is the causative agent of tuberculosis, one of the most devastating diseases. Roche patented, among other things, primer sets for polymerase chain reaction (PCR) that are complementary to the biomarker sequences, and the process of detecting the biomarkers through use of PCR.

In the past the Federal Circuit has considered other patents that claim PCR primers having natural sequences, and the process of performing PCR with them, concluding they are not patent eligible. However, this case is different: In this case the natural DNA sequence is found on a circular DNA chromosome. M. tuberculosis, like all bacteria, has a single circular chromosome, unlike eukaryotes, which have linear chromosomes. In contrast, PCR primers must be linear, or they cannot function to prime DNA polymerization during PCR.

Therefore, Roche argued that the patent claims were directed to DNA that is not identical to the natural DNA in the bacterium, and so it is not a “product of nature.” The Federal Circuit disagreed. It cited In re BRCA1- & BRCA2-Based Hereditary Cancer Test Patent Litig. for the proposition that an abbreviated segment of a longer piece of natural DNA is no different from the natural DNA. Roche pointed out that the BRCA1 & BRCA2 case involved natural DNA on a linear molecule, not natural DNA on a circular molecule, as in the case at bar. The Federal Circuit found this structural distinction to be of no importance, opining “the subject matter eligibility inquiry of primer claims hinges on comparing a claimed primer to its corresponding DNA segment on the chromosome—not the whole chromosome” (emphasis from original). This would seem to be somewhat at odds with the statement elsewhere in the opinion that the presence of a free 3’ hydroxyl group on the claimed PCR primer does not distinguish the primer from the natural DNA, as this is a chemical difference with the corresponding DNA segment. The Federal Circuit’s position could be interpreted to mean that the nucleotide sequence of the natural DNA segment is the only thing that matters, to the exclusion of any other chemical or physical property of the molecule, because courts have interpreted the nucleotide sequence to embody the “information” that is the critical function of DNA. This line of reasoning could logically be extended to ban patenting of artificial polynucleotides such as locked nucleic acid and morpholinos (although to date no court has so held). Alternatively, the decision could be read to mean eligibility requires a difference between the natural and artificial DNA that affects the functioning of the invention – in this case the circularity of the entire genome hosting the natural sequence was of no consequence to the functionality of the sequence as a PCR primer.

For the first time this decision considered whether artificial DNA with an identical sequence to what is natural, but a different higher order of structure, can be patented. This decision reaffirms that PCR performed with a primers complementing a previously unknown, but naturally occurring nucleic acid sequence, cannot be patented, regardless of whether something about the gross structure of the natural genome could have prevented its use as a primer. The reason for this conclusion seems to be that the higher level structure of the natural DNA does not affect the functioning of the claimed primer, by itself or as used in PCR. It is possible that other chemical differences between a natural DNA molecule and an artificial DNA molecule with the same sequence could still distinguish the artificial DNA from its natural counterpart.

The Roche patent in this case was drafted many years before the Supreme Court’s Myriad ban went into effect, during which time it was unquestionably patent eligible subject matter. This may be why Roche’s arguments have the definite sound of post-hoc rationalizations, because the patent was not drafted with the goal of satisfying the Myriad standard. Those present patent applicants, with the luxury of being forewarned, should consider this case a lesson. Reliance on the differences in the gross structure of the chromosome in which a natural sequence is found and the claimed DNA may be misplaced. Instead, seek to rely on differences in the primary structure (nucleotide sequence), conjugation between natural nucleic acids (DNA and RNA) with synthetic moieties (such as fluorophores, etc.), or chemical differences in the nucleotides themselves (such as LNA or triplex molecules). Last but not least, remember that the Myriad ban is not the law in most major jurisdictions outside of the United States, and consider such foreign markets when planning your patenting strategy.

Federal Circuit Holds Notebook-Tabbed Spreadsheets Are Patent EligibleIn recent years, the Federal Circuit has issued a number of decisions attempting to define the line between computer-implemented claims that are patent ineligible under 35 U.S.C. § 101 for being directed to an abstract idea with no inventive concept applied to it and eligible claims directed to more than simply an abstract idea. The Federal Circuit’s recent decision in Data Engine Technologies LLC v. Google LLC illustrates both types and the key distinctions between them: moving beyond claiming a highly generalized concept or desired result and instead claiming specific structures or implementations that improve computer functionality.

In Data Engine Technologies, the Federal Circuit affirmed in part and reversed in part the district court’s ruling that claims directed to aspects of electronic spreadsheets were not patent-eligible subject matter. The Federal Circuit distinguished patent-eligible claims “directed to a specific improved method for navigating through complex three-dimensional electronic spreadsheets” from ineligible claims “directed to the abstract idea of collecting, recognizing, and storing changed information” or “identifying and storing electronic spreadsheet pages.”

The Asserted Patents

The patents at issue, U.S. Patent Nos. 5,590,259; 5,784,545; 6,282,551; and 5,303,146, all relate to electronic spreadsheets. The ’259, ’545, and ’551 patents (Tab Patents) specifically relate to the use of notebook tabs to navigate through three-dimensional electronic spreadsheets. As explained by the court, the Tab Patents “identify problems with navigation through prior art three-dimensional or multipage electronic spreadsheets” and “claim a method of implementing a notebook-tabbed interface, which allows users to easily navigate through three-dimensional electronic spreadsheets.” Claim 12 of the ’259 patent is representative:

12. In an electronic spreadsheet system for storing and manipulating information, a computer-implemented method of representing a three-dimensional spreadsheet on a screen display, the method comprising:

displaying on said screen display a first spreadsheet page from a plurality of spreadsheet pages, each of said spreadsheet pages comprising an array of information cells arranged in row and column format, at least some of said information cells storing user-supplied information and formulas operative on said user-supplied information, each of said information cells being uniquely identified by a spreadsheet page identifier, a column identifier, and a row identifier;

while displaying said first spreadsheet page, displaying a row of spreadsheet page identifiers along one side of said first spreadsheet page, each said spreadsheet page identifier being displayed as an image of a notebook tab on said screen display and indicating a single respective spreadsheet page, wherein at least one spreadsheet page identifier of said displayed row of spreadsheet page identifiers comprises at least one user-settable identifying character;

receiving user input for requesting display of a second spreadsheet page in response to selection with an input device of a spreadsheet page identifier for said second spreadsheet page;

in response to said receiving user input step, displaying said second spreadsheet page on said screen display in a manner so as to obscure said first spreadsheet page from display while continuing to display at least a portion of said row of spreadsheet page identifiers; and

receiving user input for entering a formula in a cell on said second spreadsheet page, said formula including a cell reference to a particular cell on another of said spreadsheet pages having a particular spreadsheet page identifier comprising at least one user-supplied identifying character, said cell reference comprising said at least one user-supplied identifying character for said particular spreadsheet page identifier together with said column identifier and said row identifier for said particular cell.

The ’146 patent relates to “methods that allow electronic spreadsheet users to track their changes.” Claim 1 of the ’146 patent is representative:

In an electronic spreadsheet system for modeling user-specified information in a data model comprising a plurality of information cells, a method for automatically tracking different versions of the data model, the method comprising:

(a) specifying a base set of information cells for the system to track changes;

(b) creating a new version of the data model by modifying at least one information cell from the specified base set; and

(c) automatically determining cells of the data model which have changed by comparing cells in the new version against corresponding ones in the base set.

The District Court Decision

Data Engine Technologies asserted various claims of the Tab Patents and the ’146 patent against Google. Google sought dismissal of all claims under Rule 12(c) on the grounds that all asserted claims were ineligible under 35 U.S.C. § 101. The district court granted that motion in its entirety. The court found that the Tab Patents were “directed to the abstract idea of using notebook-type tabs to label and organize spreadsheets” and lacked any inventive concept to confer eligibility. Similarly, the court found that the ’146 patent “was directed to the abstract idea of collecting spreadsheet data, recognizing changes to spreadsheet data, and storing information about the changes” and again lacked any inventive concept. Data Engine Technologies appealed.

The Federal Circuit Decision

The Federal Circuit applied the standard two-step test from Alice Corp.: 1) whether the claims are directed to a patent-ineligible concept and, if so, 2) whether an element or combination of elements in the claim provides an “inventive concept” that amounts to more than a patent on the ineligible concept itself.

Beginning with the Tab Patents, the Federal Circuit disagreed with the district court’s conclusion that the claims were directed to the abstract idea of using notebook tabs to organize a spreadsheet. Instead, the court concluded that representative claim 12 was directed “to a specific method for navigating through three-dimensional electronic spreadsheets.” The Tab Patents identified a “known technological problem in computers”—the complexity of navigating and using prior art electronic spreadsheets—and then described and claimed a specific solution to that problem—providing user-friendly notebook tabs to navigate the spreadsheet. Rather than claim “the idea of navigating through spreadsheet pages using buttons or a generic method of labeling and organizing spreadsheets,” the Tab Patents claimed “a specific interface and implementation” that provided a “technical solution and improvement in computer spreadsheet functionality” that was lauded in the industry at the time.

In that respect, the claims were similar to those at issue in the Federal Circuit’s prior decision in Core Wireless Licensing S.A.R.L. v. LG Electronics, Inc. In that case, the court held that claims directed to an improved display interface were patent-eligible because the claimed invention “increased the efficiency with which users could navigate through various views and windows.” In both instances, the claims were directed to a particular implementation that improved existing technology.

Google argued the claims were no different than those in several Federal Circuit decisions in which the court held that claims directed to methods of organizing and presenting information are abstract. The court found all of those cases to be distinguishable because those claims lacked “any specific structure or improvement of computer functionality.” On the other hand, reading the claim as a whole as Alice requires, claim 12 moved beyond simply claiming the manipulation or organization of information to improve navigation in electronic spreadsheets and claimed “a specific structure (i.e., notebook tabs)” to perform “a specific function (i.e., navigating within a three-dimensional spreadsheet).”

The Federal Circuit did, however, reach a contrary conclusion as to one claim of the Tab Patents. The court concluded that claim 1 of the ’551 patent did not claim “the specific implementation of a notebook tab interface.” Instead, it generically claimed associating a spreadsheet with a user-settable page identifier and thus was directed to “the abstract idea of identifying and storing electronic spreadsheet pages.” Because the claim was “not limited to the specific technical solution and improvement” found in the remaining claims of the Tab Patents, claim 1 was directed to an ineligible abstract idea. Considering the claim as a whole, the court could find no inventive concept. Thus, the Federal Circuit affirmed the district court’s decision that claim 1 was not directed to patent-eligible subject matter.

The Federal Circuit reached the same conclusion as to the ’146 patent. The court agreed with the district court’s assessment that representative claim 1 was “directed to the abstract idea of collecting spreadsheet data, recognizing changes to spreadsheet data, and storing information about the changes.” The court found nothing in claim 1 that “improve[d] spreadsheet functionality in a specific way sufficient to render the claims not abstract.” Concluding that the ’146 patent claims included only generic steps and lacked any inventive concept, the Federal Circuit affirmed the district court’s decision that the claims of the ’146 patent were not directed to patent-eligible subject matter.

This decision underscores that an applicant seeking to avoid Alice eligibility problems for a computer-implemented invention should focus on defining a technological problem and claiming a specific implementation that solves that problem and improves computer functionality. Broad and generic claims covering any and all implementations of an abstract desired result will continue to be vulnerable under Alice. On the other hand, those alleged to infringe generic, abstract claims should pursue an Alice-based motion to bring litigation to a conclusion as early as practicable.

Inventors of methods of medical testing have had a rough time since the Supreme Court decided Mayo Collaborative Services v. Prometheus Labs. Inc. In the Mayo case, the Court considered whether a method of determining whether a patient is receiving the proper dosage of thioguanine drugs is eligible for patenting, when the method involved measuring the concentration of a specific metabolite of thioguanine in the patient’s blood. The inventor had determined the safe range of dosages was not based not on the dosage itself (which varied a great deal from person to person), but depended on the concentration of the metabolite. The Court concluded that the patent merely claimed a relationship between metabolite concentration, safety, and efficacy of the drug, which without more is not an invention.

Since Mayo was decided, courts have invalidated numerous medical testing patents as subject matter that is not eligible for patenting (See, e.g., Cleveland Clinic Foundation v. True Health Diagnostics, LLC, Genetic Tech. Ltd. v. Merial LLC, Ariosa Diagnostics, Inc. v. Sequenom, Inc., SmartGene, Inc. v Advanced Biological Labs.,  and PerkinElmer Inc. v Intema Ltd.).

A Rare Win for a Medical Testing Patent in <i>Exergen Corporation V. Kaz USA, Inc.</i>This makes the recent decision by a panel of the U.S. Court of Appeals for the Federal Circuit in Exergen Corp. v. Kas USA, Inc. something of a unicorn. Exergen patented a forehead thermometer that functions by measuring the radiative output of the skin at least three times per second, identifying a peak temperature that indicates that the thermometer has passed over an artery, and executing an algorithm based on the peak temperature and the ambient air temperature to calculate the patient’s core body temperature. Some of the asserted patent claims included the limitation that the artery is the temporal artery (located in the side of the forehead). The Exergen thermometer has the advantage over prior art thermometers of measuring a patient’s core temperature noninvasively, a benefit every parent can appreciate. Several companies, including Kaz, offered similar forehead thermometers, and Exergen filed several infringement suits in the U.S. District Court for the District of Massachusetts, which were consolidated only for claim construction purposes. Among other defenses, Kaz alleged that all of Exergen’s asserted patent claims were invalid as non-eligible subject matter for patenting under the Mayo decision.

The Trial Court Decision

At trial the judge ruled from the bench that the asserted claims were eligible subject matter as a matter of law. The jury found that Kaz infringed the patents and awarded damages. On appeal Kaz argued that the trial court had impermissibly decided the question of patent eligibility without sending the relevant factual questions to the jury, and, in the alternative, that Exergen’s claims were not patent eligible as a matter of law.

The Appellate Decision

Among the claims at issue were both method claims and apparatus claims. Claim 24 of the ‘685 was considered by the appellate court as typical of the apparatus claims, and reads as follows:

A body temperature detector comprising:

a radiation detector; and

electronics that measure radiation from at least three readings per second of the radiation detector as a target skin surface over an artery is viewed, the artery having a relatively constant blood flow, and that process the measured radiation to provide a body temperature approximation, distinct from skin surface temperature, based on detected radiation.

Note that the electronics are defined mainly by their function. Claim 14 of the ‘938 was considered by the appellate court as typical of the method claims, and reads as follows:

  1. A method of detecting human body temperature comprising

making at least three radiation readings per second while moving a radiation detector to scan across a region of skin over an artery to electronically determine a body temperature approximation, distinct from skin surface temperature.

The court applied the general test in Alice for patent eligibility (readers of this blog can review the Alice test here). The court found that the claims fell under the categories of subject matter Congress intended should be patented, as expressed in 35 U.S.C. § 101, as “machines” and “processes.” The court went on to conclude the claims were “directed to” one of the judge-made exceptions to the statutory categories, specifically the “law of nature” that physiologic core temperature is a function of skin temperature above an artery and ambient temperature. Based on these two conclusions, a claim would not be eligible for patenting unless as a whole it encompasses “substantially more” than natural law itself.

Kaz argued that the claims were not substantially more than the simple recognition of the relationship between skin temperature above an artery, ambient temperature, and core temperature. In Kaz’s view, the remaining parts of the claims were “conventional, well understood” elements. In support of this argument, Kaz cited the undisputed fact that the use of infrared radiation measurements of the skin to detect internal injuries was known before Exergen’s invention, and such measurements were made at a rate exceeding three readings per second.

The appellate court disagreed with Kaz’s argument and affirmed the district court’s finding that the claims were directed to substantially more than the natural law. Regarding the older method of detecting internal injury, the court pointed out that “Something is not well-understood, routine, and conventional merely because it is disclosed in a prior art reference… This case is not like either Mayo or Ariosa, where well-known, existing methods were used to determine the existence of a natural phenomenon.” In other words, the inventors in Mayo and Ariosa identified the relationship between an analyte and a condition, and claimed measuring the analyte by only well-understood, routine, and conventional methods (in Mayo the broadest claims were not specific to the measurement methods at all). Exergen’s claims included an unconventional method of determining core body temperature, which was novel independent of the recognition of the specific relationship between the temperature of the skin above an artery and the patient’s core body temperature. Although body radiation sensors were known, none had been configured to convert skin temperature to core temperature; although methods of measuring skin temperature with a radiation sensor were known, none had specifically measured skin temperature above and artery and converted it to core temperature.

How Does Exergen Fit with Current Case Law?

Comparing Exergen to Mayo, in Mayo the measurement of the metabolite was claimed generally, not by any specific method, conventional or otherwise. Measuring the metabolite was well-known and conventional. The claims in Mayo thus involved only a well-known and conventional step, in combination with reaching a diagnosis. Although the criteria used for the diagnosis were not previously known, others had tried to use the metabolite concentration to diagnose the same condition using different criteria. In contrast, Exergen claimed steps that had never been performed before — measuring skin temperature over an artery by radiometry, in addition to the more abstract steps of calculating core temperature.

The distinctions between this case and Ariosa are more subtle, and the two cases might seem inconsistent. The patent in Ariosa did claim steps that had never been performed before; namely, it recited amplifying paternal DNA in a maternal whole blood sample. The court focused on the fact that the paternal DNA was claimed to be measured by conventional methods (polymerase chain reaction), so that nothing substantial was added to the concept of measuring the paternal DNA itself. In Exergen, the court defined the measured property as body core temperature, and found that it was neither routine nor conventional to measure body core temperature as claimed. However, if the court had considered ultra-arterial skin temperature to be the measured property, instead of core temperature, it might have concluded that the claimed steps were conventional and well-understood ways of measuring it.

This distinction can serve as guidance going forward: Defining exactly what is being measured can be determinative of the Alice analysis of medical tests. Those seeking to patent or defend medical testing claims could benefit from defining the measured property narrowly. Alternatively, those seeking to invalidate medical testing patents should seek to define the measured property broadly as something that has been measured before in the same way. For example, does the invention measure core temperature by measuring ultra-arterial skin temperature by radiometry, or does it measure skin temperature by radiometry? The latter steps were known in the prior art, while the former were not.