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Getting Creative: Prosecuting Biotechnology Applications at the USPTO after Mayo

Cynthia M. Bouchez

©2017. Published in Landslide, Vol. 9, No. 6, July/August 2017, by the American Bar Association. Reproduced with permission. All rights reserved. This information or any portion thereof may not be copied or disseminated in any form or by any means or stored in an electronic database or retrieval system without the express written consent of the American Bar Association or the copyright holder.

It is difficult to exaggerate the effects of Mayo1 and its progeny on the biotechnology industry, particularly for diagnostic methods and gene-based therapies.2 Patent applications that easily would have stepped over the pre-Mayo § 101 bar are now facing a tall hurdle to allowance at the U.S. Patent and Trademark Office (USPTO). Patent prosecutors and the USPTO have settled into this reality, having realized that the courts are not going to come to the rescue any time soon, if at all.

In response to the changes in patent eligibility law, the USPTO extensively retrained its examining corps. To that end, the USPTO has issued guidelines, updates to guidelines, training slides, examples, indices of examples, case law summaries, and memoranda, in addition to holding forums and roundtable discussions and requesting and receiving written comments. The USPTO has the difficult and complicated tasks of engaging stakeholders in formulating its examination guidelines and issuing patents that comply with existing law. Patent prosecutors have the similarly difficult task of navigating the examination guidelines, Patent Trial and Appeal Board (PTAB) decisions, and Federal Circuit and Supreme Court case law. In light of the arguably inconsistent decisions from the courts,3 stakeholders have also found confusion at the USPTO. In recent comments submitted to the USPTO, the American Intellectual Property Law Association (AIPLA) sums up the state of affairs in prosecuting applications under the new patent eligibility regime: “Overall, our experience is that Patent Office examination decisions on patent eligibility have been inconsistent and confusing.”4 Patent practitioners thus have no choice but to be creative in prosecuting biotechnology patents where subject matter eligibility is an issue.

The USPTO’s Response to Changes in Patent Eligibility Law

In December 2014, the USPTO issued interim guidance on patent subject matter eligibility, which provides analysis for claims reciting judicial exceptions in view of Mayo and related cases.5 The 2014 guidance provides a flow chart that includes steps 1, 2A, and 2B. Step 1 simply asks if the claim is directed to a process, machine, manufacture, or composition of matter. If so, the examiner proceeds to step 2A, which is part 1 of the Mayo test, and asks whether the claim is “directed to” a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea. Step 2B asks whether the claim recites additional elements that “amount to significantly more” than the judicial exception. The flowchart instructs that claims directed to nature-based products should be evaluated in step 2A. The analysis compares the nature-based product of the claim to its naturally occurring counterpart to identify markedly different characteristics. These characteristics can be based on structure, function, and/or properties.

In July 2015, the USPTO issued an update to its guidance to reflect public comments.6 A further update issued in May 2016, which informed the examining corps of best practices for formulating a subject matter eligibility rejection and evaluating the applicant’s response.7 The USPTO also issued specific memoranda in light of subject matter eligibility decisions from the Federal Circuit. Along with the guidelines, the USPTO issued biotechnology-related examples on December 16, 2014; March 6, 2015; and May 4, 2016. These materials are collectively referred to as “the Guidance.”8 The USPTO also has established a group of subject matter experts who can be consulted on cases involving ineligibility rejections.

Using the Guidance During Prosecution

The Guidance does not constitute substantive rulemaking and does not have the force and effect of law. This begs the question: how much does the Guidance matter? In other words, as practitioners we must consider whether it is worth attempting to persuade examiners to adhere to the Guidance. Like with most prosecution strategies, the answer depends at least in part on the examiner and on the particular pending claims. It may be worthwhile to push back on an examiner’s rejection with the Guidance if the pending claim closely tracks an allowable claim in the examples of the Guidance. The Guidance instructs examiners not to use the examples as a basis for the rejection, but acknowledges that it is acceptable for an applicant to cite an example in rebuttal.9 The Guidance further instructs examiners that applicants should not be required to model their claims or responses after the examples.10 Thus, the Guidance may also be helpful to rebut an examiner who requires that a claim be amended to conform to an example in the Guidance.

The Guidance can also be used to challenge an examiner on step 2B of the Mayo test, i.e., establishing steps as “routine or conventional.” The Guidance emphasizes that a new combination of steps in a process may be patent eligible even though all the steps were individually known and in common use. Thus, reminding examiners of this aspect of the Guidance may be helpful in advancing prosecution.

Ideally, the Guidance should be used in tandem with arguments focused on the case law. As the AIPLA has pointed out, “Examiners are not trained to make the fine distinctions that appear in judicial opinions, and should not be expected to do so.”11 However, as practitioners, we should engage with examiners to discuss details of cases that are being used in a patent ineligibility argument. Examiners should be asked to focus on the specific claim language in the case law and the distinctions between that language and the pending claims.

The PTAB sometimes discusses the Guidance in its decisions, particularly if the examiner and/or applicant relies on them in their own arguments. For instance, the PTAB database contains 18 final decisions for ex parte appeals from subject matter eligibility rejections in Technology Center 1600 (Biotechnology and Organic Chemistry) from the beginning of 2017 to mid-March 2017. The Guidance was mentioned in eight of those decisions.

In one such instance, the claim was directed to a composition for enabling self-renewal of pluripotent human stem cells, comprising a substrate, a coating, and a chemically defined medium.12 The examiner stated that the claim limitations did not render the composition markedly different in structure from a naturally occurring product, and thus the claims were ineligible under § 101. The appellants argued that the non-naturally occurring elements, i.e., the substrate, the coating, and the chemically defined medium, amounted to significantly more than the judicial exception.13 The appellants analogized to one of the examples in the Guidance: “claim 1 is quite similar to claim 5 of . . . Example 9 of the Examples: Nature-Based Products issued on December 16, 2014 [and] claim 5 was found to be eligible because the combination of the cells in the scaffold confined the claim to a particular useful application (repair of cardiac tissue), and improved the technology.”14

In reversing the examiner’s rejection under § 101, the PTAB’s decision specifically discusses example 9 of the Guidance, stating: “The instant claims are similar to Example 9 because the pluripotent human stem cells are not recited as growing on any substrate, but rather a particular substrate coated with intact recombinant laminin-511 along with a chemically defined medium (see claims 1 and 5).”15

To be sure, in this decision, the PTAB also cites Supreme Court and Federal Circuit case law to support its position, but also gives at least a nod to the Guidance.

On the other hand, in another recent decision, the PTAB noted that “[a]s an initial matter, . . . the March 2014 Guidance is not law and also does not reflect the USPTO’s current analysis protocols on subject matter eligibility.”16 Here, the PTAB minimizes the importance of the Guidance, but it may have done so because the appellants cited an outdated version of the Guidance.

For methods of detecting biomarkers, it may be worthwhile to focus the examiner’s attention on the “Julitis” example 29 of the Guidance. This example indicates that methods of detecting biomarker claims are eligible, but adding steps that fall under a judicial exception will make it ineligible.17 The example explains that a method of detecting “JUL-1” in a patient is eligible if the steps comprise obtaining a sample from the patient and detecting whether JUL-1 is present in the plasma by contacting the plasma sample with an anti-JUL-1 antibody, and detecting binding. Analogizing to Mayo, the Guidance reasons that this detecting the biomarker claim does not contain a judicial exception because “recited steps of administering a drug to a patient and determining the resultant level of 6-thioguanine in the patient ‘are not themselves natural laws.’”18

However, if the claim is reframed as a diagnostic claim containing the same steps as the detecting the biomarker claim, but adds “diagnosing the patient with julitis,” then the Guidance indicates this is not patent eligible. Here, the Guidance reasons that the diagnosing step is a judicial exception because (1) the correlation is a consequence of natural processes, similar to the naturally occurring correlation found to be a law of nature in Mayo; and (2) this step could be performed by a human using mental steps, citing Ambry19 and Grams.20 A potential solution may be to rephrase “diagnosing” as “communicating” or some equivalent. Although this will likely avoid the mental step objection, this may not avoid the correlation aspect of the objection to the claim.

Putting aside the subject matter ineligibility issue, a practitioner may not wish to include a diagnosing step to avoid a potential split infringement issue. A laboratory typically performs the “detecting” steps, and a doctor performs a “diagnosing” step. The relationship between the parties may not be sufficient to establish infringement under the new regime.21 A thorough discussion of split infringement is beyond the scope of this article, but must always be kept in mind during prosecution.

In sum, the Guidance should be used in moderation because it does not have the force of law. If an examiner is resisting adherence to the Guidance, the best tactic is to refocus on the case law and the specific claim language or use the additional strategies outlined below.

Lessons from Recent PTAB Decisions

Citing PTAB decisions during prosecution should also be considered in response to an examiner’s ineligible subject matter rejection. PTAB decisions are rarely designated as precedential, which would be binding on all members of the PTAB. All other PTAB opinion designations—i.e., informative, representative, and routine—are not binding authority. Most opinions are “routine.” Nevertheless, even routine PTAB opinions can be helpful to applicants because there are far more of these opinions than those at the Federal Circuit or Supreme Court. Further, an examiner may be more inclined to be persuaded by these opinions because the PTAB hears appeals from examiner’s rejections.

Ex parte Terbrueggen is a recent PTAB opinion that may be useful to biotechnology practitioners.22 Here, the PTAB reviewed claims directed to a method for detecting target nucleic acids in a sample, in which two probes to distinct portions of a target hybridize to the target in a manner allowing chemical ligation of the probes.23 The ligation product is then amplified. A third probe is used to capture the ligation product on the surface.24 The PTAB reversed the rejection under § 101 as being directed to ineligible subject matter.

The examiner reasoned that the “method of detecting” step is an abstract idea, and therefore a judicial exception.25 The examiner further explained that the detecting step can be “performed by simply looking at a result, or reading a report.”26 The PTAB disagreed that the detecting step is an abstract idea. Rather, the PTAB concluded that the language of the claim requires actual physical detection of amplified nucleic acids.27 Some physical action must be performed to determine the presence of the nucleic acids, citing as evidence the specification’s recitation of several specific techniques for the detecting step.28

The PTAB further explained that the examiner did not properly evaluate the claim as a whole in determining that the claimed invention uses nothing more than conventional steps to implement the alleged abstract idea.29 Rather, even if it were true that the individual steps of the claimed process were known in the art, the PTAB concluded that the examiner failed to provide evidence that the claims are not novel and/or unobvious.

This case underscores the importance of including specific and technical information in the specification to rebut an assertion of abstract ideas or mental steps. In this regard, computer-implemented methods may be on similar footing with biotechnology inventions, where, for example, including the details of an algorithm may save a patent from ineligibility.30

Although the PTAB recently issued a few decisions that reversed § 101 rejections in Technology Center 1600, the majority of decisions uphold the examiner’s rejections. For example, this year at least two method of treatment claims in the personalized medicine context were found patent ineligible.31 A method for detecting a toxic strain of bacteria was also found ineligible under § 101.32 Each of these applications was filed before Mayo, so although the decisions uphold the patent ineligibility rejections, they may be helpful in guiding practitioners moving forward.

Getting Creative with New Strategies: Review Other Patentability Criteria

Speaking on behalf of its membership, the AIPLA recently advised the USPTO that:

As applied . . . section 101 too often has been used as an easy, blunt instrument to deny patent protection. In such cases, other grounds for finding patent claims invalid (or claims in an application unpatentable) more prudently could be based on prior art and other conditions of patentability set forth in sections 102, 103 and 112.33

Addressing this concern, one strategy for prosecution is to request that the examiner first consider all other patentability criteria under §§ 102, 103, and 112. Only following resolution of those issues should the examiner take up the discussion of patent eligibility under § 101. It may be more difficult for an examiner to assert that steps are “routine and unconventional” if the claims are free of the art. In the majority of recent PTAB decisions where patent eligibility was appealed, the appealed claims were rejected under other grounds as well. It is worth considering whether overcoming the prior art issues would have also eliminated the subject matter ineligibility rejection as well.

This strategy also may give the examiner some confidence in allowing the claim, knowing that the other patentability criteria have been met. Also, as noted earlier, § 101 case law is confusing and arguably contradictory. It is easy to get bogged down in the patent eligibility morass, and setting it aside for later discussion may end up expediting prosecution.

Getting Creative with Familiar Strategies: Declarations and Interviews

In addressing subject matter eligibility rejections, patent prosecutors have a variety of familiar tools at their disposal. For example, practitioners should consider filing expert declarations under 35 C.F.R. § 1.132 to rebut a patent ineligibility rejection. This approach may be counterintuitive because practitioners typically think of § 101 as a purely legal issue, beyond the purview of technical experts.34 But given the conflation of § 101 and §§ 102 and 103, technical declarations can be used in the same way that they are submitted to rebut obviousness rejections. For instance, a technical expert declaration should be considered to rebut an assertion that steps are “routine or conventional” in step 2B of the USPTO’s Mayo analysis. Indeed, in 2016, a group director at the USPTO indicated that he expected to see more affidavits regarding subject matter eligibility, indicating that the USPTO is at least open to an expert’s factual findings in this context.35

In-person interviews and telephonic interviews are a familiar and useful tool in the patent prosecution arsenal. They are perhaps even more critical when faced with a subject matter rejection because the presence of a USPTO subject matter expert at the interview can be helpful in resolving issues in real time. Examiners often confer with these experts regardless. Having all parties at the table can obviously expedite decision making. During the interview, practitioners should not hesitate to ask if adding specific claim language would overcome the subject matter ineligibility rejection. Anecdotally, it appears that some art units may have agreed on amendments that will overcome some § 101 rejections.

If the claims are such that a patent ineligibility rejection is likely, it may be worth considering the First Action Interview Pilot Program (FAIP). The program is free, but the application must contain no more than 20 claims and no more than three independent claims. Additional claims can be added later, however. A FAIP request must be filed before a first office action. Once the request is accepted, the examiner performs an initial search and prepares a pre-interview communication. An applicant has one month to respond with an interview request form with an agenda and/or proposed amendment. After the interview is conducted, the examiner either allows the case or issues a first action interview office action summary. The applicant then has two months to respond to the summary, and prosecution continues as usual. According to the USPTO Data Visualization Center, the FAIP first action allowance rate has been about twice the first action allowance rate in new, noncontinuing applications.36

A disadvantage of this program is that the first action interview office action summary takes the place of a full first office action, but often does not contain the detail in a typical first office action. If agreement is not reached, the next office action is often designated as final. The benefits of interviewing the examiner on subject matter eligibility issues before a full office action may outweigh this disadvantage.


The seismic shift in § 101 law has left practitioners and the USPTO struggling to determine effective strategies to obtain patents directed to worthy biotechnology inventions. Hopes for additional clarity for diagnostic claims were dashed upon denial of certiorari in Sequenom v. Ariosa.37 Until (and if) Congress acts, companies, their legal advisors, and the USPTO must work within the current regime, using both unfamiliar and familiar strategies in creative ways to obtain allowances of biotechnology inventions.


1. Mayo Collaborative Servs. v. Prometheus Labs., Inc., 132 S. Ct. 1289 (2012).

2. See, e.g., Michael A. Sanzo, Lengthening Shadows: Biotechnology and Patent Eligibility, 9 Landslide, no. 5, May–June 2017.

3. See, e.g., Letter from Donna P. Suchy, Section Chair, ABA Section of Intellectual Prop. Law, to Michelle K. Lee, Under Sec’y of Commerce for Intellectual Prop. & Dir., USPTO, Request for Comments Related to Patent Subject Matter Eligibility 2 (Jan. 18, 2017),

4. Letter from Mark L. Whitaker, President, AIPLA, to Michelle K. Lee, Under Sec’y of Commerce for Intellectual Prop. & Dir., USPTO, Comments of the AIPLA on Notice of Roundtables and Request for Comments Related to Patent Subject Matter Eligibility, 81 Fed. Reg. 71485, 10/17/2016, at 1 (Jan. 18, 2017), [hereinafter AIPLA Comments].

5. 2014 Interim Guidance on Patent Subject Matter Eligibility, 79 Fed. Reg. 74,618 (Dec. 16, 2014).

6. July 2015 Update on Subject Matter Eligibility, 80 Fed. Reg. 45,429 (July 30, 2015).

7. May 2016 Subject Matter Eligibility Update, 81 Fed. Reg. 27,381 (May 6, 2016).

8. See Subject Matter Eligibility, USPTO, (last modified Apr. 26, 2017).

9. Memorandum from Robert W. Bahr, Deputy Comm’r for Patent Examination Policy, to Patent Examining Corps, Formulating a Subject Matter Eligibility Rejection and Evaluating the Applicant’s Response to a Subject Matter Eligibility Rejection 5 (May 4, 2016),

10. Id.

11. AIPLA Comments, supra note 4, at 7.

12. Ex parte Tryggvason, No. 2016-001857, slip op. at 2 (P.T.A.B. Jan. 26, 2017).

13. Id. at 12.

14. Id.

15. Id. at 13.

16. Ex parte Park, No. 2015-007714, slip op. at 6 (P.T.A.B. Feb. 23, 2017).

17. Some commentators have rightly criticized this example because the narrower claim (diagnostic claim) could depend from the broader claim (detecting biomarkers), yet be ineligible. The example also concludes that diagnosing is a mental step, yet the case law may not support this viewpoint. See, e.g., Suzannah K. Sundby, 101 Guidelines & Case Law in Biotech & Precision Medicine: How Far Have We Come?, AIPLA Webinar (Jan. 24, 2017),

18. Subject Matter Eligibility, supra note 8 (follow “Life sciences examples 28–33” hyperlink under “Examples”) (citing Mayo Collaborative Servs. v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1297 (2012)).

19. In re BRCA1 – and BRCA2-Based Hereditary Cancer Test Patent Litig. (Ambry), 774 F.3d 755 (Fed. Cir. 2014).

20. In re Grams, 888 F.2d 835 (Fed. Cir. 1989).

21. See, e.g., Jorge A. Goldstein & Cynthia M. Bouchez, Personalized Medicine Patents in Great Legal Turmoil, 18 Intell. Prop. Today, no. 8, Aug. 2011, at 18.

22. No. 2017-001359 (P.T.A.B. Jan. 18, 2017).

23. Id., slip op. at 5.

24. Id.

25. Id. at 9.

26. Id.

27. Id. at 10.

28. Id.

29. Id. at 11.

30. Dennis Crouch, Eligibility: Get Technical or Get Denied, Patently-O (May 15, 2017),

31. Ex parte Penger, No. 2015-007994 (P.T.A.B. Feb. 2, 2017); Ex parte Chamberlain, No. 2014-009849 (P.T.A.B. Jan. 20, 2017).

32. Ex parte Van Den Bogaard, No. 2016-003313 (P.T.A.B. Jan. 31, 2017).

33. AIPLA Comments, supra note 4, at 2.

34. But see Icon Health & Fitness, Inc. v. Strava, Inc., 849 F.3d 1034 (Fed. Cir. 2017) (finding no error in relying on an expert’s declaration where that declaration made legal conclusions in addition to factual findings).

35. Jennifer Spaith & Christopher Ziolkowski, Sequenom, Alice and Mayo in 2016, Westlaw J. Intell. Prop. (2016),

36. Data Visualization Center, USPTO, (last visited May 23, 2017).

37. See Sequenom, Inc. v. Ariosa Diagnostics, Inc., SCOTUSblog, (last visited May 23, 2017).

Cynthia M. Bouchez

Cynthia M. Bouchez is a partner at Medler Ferro in McLean, Virginia. She specializes in worldwide patent strategies, due diligence investigations, freedom-to-operate analyses, and validity, infringement, and patentability opinions.