USPTO Updates Guidance on Patent-Eligibility of Personalized Therapy

12 November 2019 Personalized Medicine Bulletin Blog
Authors: Antoinette F. Konski

In an October 17, 2019 update (“2019 Update”) of its current subject matter eligibility guidance (2019 Revised Patent Subject Matter Eligibility Guidance (“2019 PEG”)), the United States Patent and Trademark Office (“USPTO”) gave further instruction on the eligibility of certain personalized therapies.

Treating Kidney Disease (Example 43)

The 2019 PEG revamped the basic analysis for claims that may recite an abstract idea from a case-comparison approach to grouping or characterizing a claim into one or more groupings of abstract ideas. 2019 Update at page 2. This approach shifted the focus from relying on individual judicial decisions to applying a body of appellate and U.S. Supreme Court case law spanning all technologies and claim types. Id.

Example 43 of the 2019 Update (Available in Appendix 1 to 2019 Update or “App. 1”) exemplifies the treatment of a hypothetical condition that relies on a pre-treatment diagnostic. The hypothetical condition - Nephritic Autoimmune Syndrome Type 3 (NAS-3) – is an autoimmune disease that primarily affects the glomeruli in the kidney. Kidney glomeruli are used to filter waste materials out of the bloodstream and NAS-3 is associated with the undesired formation of a protein complex in the glomeruli that can ultimately lead to chronic kidney disease or failure.

Treatment of NAS-3 is complicated because it progresses rapidly, and some patients do not respond well to glucocorticoids (a class of steroids), which are the conventional first-line therapy. Those patients who are non-responsive to glucocorticoids may respond to conventional second-line treatments, which include administration of non-steroidal agents such as rapamycin. Another conventional second-line treatment for some patients is a course of plasmapheresis, which is a filtration process that removes excess autoantibodies from the patient’s blood. Due to the significant risk with second-line treatment, it is only advised if the patient is non-responsive to first-line glucocorticoids.

According to the hypothetical, the invention lies in the discovery of a ratio between the levels of two proteins found in the blood of NAS-3 patients – C11 and C13. The specification discloses that a high ratio (greater than 3:1) of C11 to C13 indicates that the patient is a non-responder to first-line therapy. Thus, a patient’s treatment is adjusted based on his or her status as a responder or a non-responder.

The hypothetical claims of Example 43 recite:

  1. A treatment method comprising:

    calculating a ratio of C11 to C13 levels measured in a blood sample from a patient diagnosed with Nephritic Autoimmune Syndrome Type 3 (NAS-3) to identify the patient as having a non-responder phenotype; administering a treatment to the patient having a non-responder phenotype.


  2. The method of claim 1, wherein the treatment is a non-steroidal agent capable of treating NAS-3.

  3. The method of claim 1, wherein the treatment is rapamycin.

  4. The method of claim 1, wherein the treatment is a course of plasmapheresis.

  5. A treatment method comprising administering rapamycin to a patient identified as having Nephritic Autoimmune Syndrome Type 3 (NAS-3)

Claim 1 – Ineligible

The claims must be analyzed under a “broadest reasonable interpretation” standard or “BRI.” Under BRI, Claim 1 is interpreted to be directed to testing a patient for responder or non-responder status by calculating the ratio of C11 to C13 levels, and then treating non-responders (i.e., the patient having a calculated ration of 3:1 or greater). No particular treatment is required by claim 1.

Under Step 1 of the current two-part eligibility test, the claim is first analyzed to determine if it recites a statutory class of patentable subject matter. Here, the claims are directed to a process that is a recognized class of patentable subject matter. The analysis then proceeds to Step 2A, Prong 1.

Under Step 2A, Prong 1 of the eligibility test, a claim is analyzed to determine if it recites a judicial exception. Here the calculation step recites an abstract idea because it requires the calculation of C11 to C13 ratio levels. Under the 2019 PEG, the claim would fall under the “mathematical concept” grouping of abstract ideas because of the mathematical calculation (determining the ratio of C11 to C13 levels) and the “mental process” grouping of claims because it is a calculation that could be performed in the human mind.

Having determined that the claim recites a judicial exception, the analysis proceeds to Step 2A, Prong 2 of the eligibility test. Under Step 2A, Prong 2, the claim is evaluated to determine if the claim as a whole integrates the recited judicial exception into a practical application of the exception. The analysis looks to whether the claim recites additional limitations beyond the judicial exception. The elements are evaluated individually and in combination to determine if the claim as a whole integrates the exception into a practical application.

The example notes that Claim 1 recites a treatment step in addition to the abstract idea. However, it also states that although treatment is to be administered, the claim does not provide any additional information as to how the patient is to be treated, or what the treatment is, but rather covers any possible treatment for the patient. Indeed, the claim does not even require the treatment to take into consideration the outcome of the calculation step. As such, the claim does not integrate the recited judicial exception into a practical application. Therefore, the claim is directed to the judicial exception. 2019 App. at page 4.

The analysis then proceeds to Step 2B, i.e., does the claim as a whole amount to significantly more than the recited exception? Here, the example notes that the only element in addition to the judicial exception is treating the patient, which is interpreted as merely applying the judicial exception. For this reason Claim 1 fails Step 2B and the claim as a whole is ineligible. 2019 App. at page 5.

Claim 2 – 4 – Eligible

Claims 2 to 4 further define Claim 1 by increasingly specifying the treatment to be applied by the method of Claim 1. Claim 2 notes the treatment is a non-steroidal agent capable of treating NAS-3. Claim 3 defines the treatment as rapamycin, and Claim 4 defined the treatment as a course of plasmapheresis.

Unlike Claim 1, Claim 2 instructs a particular treatment or prophylaxis, even though the administration is a well-known and conventional treatment for NAS-3. However, because Step 2A Prong 2 analysis excludes consideration of whether a limitation is well-understood, routine, or conventional activity, this fact has no bearing on the eligibility analysis. Id. at page 7. The example additionally notes that because there is more than a nominal relationship between the judicial exception and the additional element, the answer to Step 2A is yes (the claim is noted to use the recited abstract idea in a manner that imposes a meaningful limit on it), citing analogy to the claims in “Endo Pharms. Inc. v. Teva Pharms. USA Inc., 919 F.3d 1347 (Fed. Cir. 2019) and Vanda Pharms. Inc. v. West-Ward Pharms. Int’l Ltd., 887 F.3d 1117 (Fed. Cir. 2018), both of which also used a judicial exception to identify patients in need of a particular treatment, and then administered the treatment.”) Id. at page 6. Claim 2 is thus patent-eligible. For similar reasons, Claims 3 and 4 also are patent-eligible.

Claim 5 - Eligible

Independent claim 5 recites:

A treatment method comprising administering rapamycin to a patient identified as having Nephritic Autoimmune Syndrome Type 3 (NAS-3). Under BRI, the claim terms are presumed to have their plain meaning. The example notes that based on the plain meaning, Claim 5 is a method of administering rapamycin to a patient having NAS-3. The claim does not require any particular dosage, mode of administration, or frequency of administration.” Id. at page 9.

Under Step 1 of the analysis, the claim is determined to be a process, which is a statutory class of invention. The analysis then proceeds to Step 2A, Prongs 1 and 2.

Under Step 2A, Prong 1, the claim is analyzed to determine if it recites a judicial exception. Here, the claim uses a natural product – rapamycin – in a method of treatment. Thus, the claim could be analyzed as a product of nature (does the nature-based product have markedly different characteristics?). However, it is noted that the general rule is that a treatment claim is not subject to the markedly different analysis for nature-based products used in the process. See MPEP 2106.04(c)(I)(C)). Id. While there are some exceptions to this rule - e.g., when the claim is drafted in way that it is no different in substance from a product claim - that exception does not apply here.

Also under Step 2A, Prong 1, the analysis asks if the claim recite a judicial exception. The example indicates that it does not, relying in part on Rapid Litig. Mgmt. v. CellzDirect, Inc., 827 F.3d 1042, 1049 (Fed. Cir. 2016), cited in MPEP 2106.04(b)(I) (a method of treating cancer with chemotherapy is not directed to the cancer cells’ inability to survive chemotherapy, and a method of treating headaches with aspirin is not directed to the human body’s natural response to aspirin). Id. Thus, Claim 5 is patent-eligible.

Personalized Therapy Is Patent-Eligible

Example 43 is a useful example for those seeking to patent treatments that use a diagnostic test. For exemplary Claims 1-4, the diagnostic test determined the ratio of protein biomarkers. In Claim 5, the patient was pre-determined to have NAS-3 and the analysis steps are not recited in the claim.

As illustrated by the analysis of Claims 1-4, general claim elements that are merely an instruction to treat a patient without any specificity will fail under the current USPTO eligibility test. More specific treatments, even if conventional and well known, may still be sufficient application of the judicial exception to confer eligibility on the claim (compare Claim 1 to Claims 2-4).

However, enforcement of Claims 2-4 may raise an issue of divided infringement as it may be necessary to invoke two separate parties to practice all elements of the claim. For example, a laboratory service provider may calculate the ratio of the C11 to C13 levels to determine if the patient has a responder or non-responder phenotype, and the physician would prescribe the specific treatment. Claim 5 avoids divided infringement because it only has one element – treatment by administration of rapamycin. However, because rapamycin is well-known and conventional, the claim may fail for lacking novelty as a separate issue.

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