Protecting Oligonucleotides and Antibodies: 3 Proven Arguments to Overcome §101 Rejections in Molecular Biology

Patent lawyers love the overused quote from Diamond v. Chakrabarty, “everything under the sun invented by man.” Forty years later, this remains good law in most situations. However, Mayo v. Prometheus and AMP v. Myriad Genetics went on to make clear that not everything under the sun is patentable when it comes to biology. Most recently, Alice, and the associated 2019 PEG have come to dominate how examiners and attorneys approach subject matter eligibility arguments, even when it comes to inventions within the life sciences.

Even with the most conscientious claim drafting, rejections under §101 are not unlikely when the claimed subject matter centers on organic molecules or other “products of nature.” Given the dynamic state of legal arguments in this field, it can be particularly helpful to look at successful responses prepared by other attorneys facing similar rejections.

If you are dealing with §101 rejections involving molecular biology, or other technology classes where “natural phenomena” are frequently cited, you may want to consider taking a prong, (or better, two), from the winning arguments we’ve selected,  below:

Molecules Created Through Human Efforts Can Lay a Path

If the subject matter is artificial, it does not fall under a judicially-created exception to §101 and, therefore, constitutes patent-eligible subject matter.

In biology cases, the examiners typically rely on the “natural phenomena” judicial exception in their §101 rejections. The Patent Office does not want to be responsible for issuing a patent on a biological matter that occurs naturally. This would potentially turn every living organism into an infringer.

To overcome this rejection under the Alice test and the 2019 examination guidelines, you must show the subject matter does not fall into the “natural phenomena” category or the claims include substantially more than a natural phenomenon. Where the claimed subject matter is artificial and the hand of an engineer or scientist is needed to produce it, the invention is legitimately the product of human ingenuity and human effort must be made to infringe the claims.

This argument succeeded in an application for a “Vesicular Linker and Uses Thereof in Nucleic Acid Library Construction and Sequencing” This case was filed in 2017 and issued in 2020.

The examiner issued a rejection under §101 citing the judicial exception for “natural phenomena.” In response, the applicant amended the claims to clarify the claimed kit did not contain a naturally occurring molecule, but rather an engineered product.

With respect to claim 3 as currently amended, the claim now recites “a first primer, having the same sequence as at least a portion of the first strand of the vesicular non-paired region of the oligonucleotide vesicular adaptor” and “a second primer, specifically paring with the second strand of the vesicular non-paired region of the oligonucleotide vesicular adaptor”. Thus, it would be appreciated by the one skilled in the art that the structures of the first primer and the second primer tightly depend on the oligonucleotide vesicular adaptor which is not a naturally occurring product and is instead is a novel and non-obvious presentation for constructing a nucleic acid library and of which specific nucleotide sequences are artificially selected in accordance with actual needs.

Specifically, the claims recited an oligonucleotide vesicular adaptor that connected to a first primer at one location and a second primer at another location. The first primer and second primer are molecules that can occur in nature. But the applicant argued the claimed kit was not a natural phenomenon for two reasons.

  1. The oligonucleotide vesicular adaptor does not occur naturally. Rather, the inventors developed this molecule.
  2. Although the molecules that make up the first primer and second primer occur in nature, a scientist must select and artificially design the first primer and second primer claimed in the application based on the application of the invention. As a result, the primers were not randomly assembled, as would occur in nature, but deliberately created, as would occur in an engineered molecule.

The examiner found these claim elements established that the claimed molecule could not occur naturally. The examiner withdrew the §101 rejection and allowed the claims.

The lesson drawn from this case is that your claims can include molecules that may occur in nature. But make sure that your claims either include non-natural molecules with them or make clear that the molecules are not the naturally occurring variety.

Kudos to Z. Peter Sawicki from Westman, Champlin & Koehler for exemplary work in drafting winning office action responses!

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A Combination of Humanized and Natural Molecules Can Save the Day

This argument is a close corollary of the first argument. If the subject matter contains molecules that are arguably naturally occurring, you may be able to argue that the combination cannot occur in nature. This moves you out of the judicial exceptions for “products of nature” and “natural phenomena” and allows you to escape the second prong of the Alice test.

Avoiding Alice’s second prong can substantially improve your chances of allowance. The test’s second prong, which asks whether the invention includes substantially more than the ineligible subject matter, is highly subjective. Therefore, qualifying under the first prong should be your first, strongest, and best thought-out argument.

This argument was used in an application for “Humanized Antibodies” This application was filed in 2016 and issued in 2020. Prior to allowance, the applicant received a rejection under §101 on the ground that the claimed invention comprised products of nature.

The antibody or antigen-binding fragment thereof of the pending claims exhibit “markedly different characteristics” as compared to a naturally occurring counterpart in at least two ways. First, one of ordinary skill in the art would understand that the non-human donor antibody is itself “man-made” … Second, … the antibody, or antigen-binding fragment thereof of claim 1, and those dependent thereon, is eligible subject matter because it exhibits structurally distinct characteristics as compared to a naturally occurring counterpart by comprising both non-human donor and human donor residues, introduced into the claimed antibody by the “hand of man.”

In response, the applicant amended the claims to clarify that the claimed invention included a humanized antibody from a non-human donor. This gave the applicant three strong arguments in the office action response:

  1. The humanized antibody behaved differently from naturally occurring antibodies. It did not behave like the non-human donor antibody because it had been humanized. And it did not behave like a human antibody because of its non-human donor origins.
  2. The humanized antibody was not naturally occurring because artificial processes were needed to humanize a non-human donor antibody.
  3. The final product, a humanized antibody, could not occur in nature because it contained both human and non-human residues.

The examiner allowed the claims. Although the examiner did not identify which of the arguments ultimately persuaded the examiner to allow the claims, all three of the arguments are powerful.

The lesson to be drawn from this case is that your chances for allowance improve if you can claim and argue for the non-natural creation, structure, and behavior of the claimed molecule.

Kudos to Elizabeth M. Rohlfs from Pfizer Inc for exemplary work in drafting winning office action responses!

A Real-World Application Can Carry You Through

Although you would prefer to satisfy the Alice test’s first prong rather than battling over the more subjective second prong, you should not limit your arguments to the first prong. If an examiner disagrees with your arguments under the first prong, you will need to present something under the second prong to try to satisfy the Alice test.

This occurred in an application for “Predicting the Ability of Atlantic Salmon to Utilize Dietary Pigment Based on the Determination of Polymorphisms” This application was filed in 2016 and allowed in 2020, although it has not yet issued as a patent because the applicant has not paid the issue fee.

The application claimed a process for sequencing the genes of an Atlantic salmon to detect cytosine at a particular location in the gene sequence. The examiner rejected these claims as directed to a natural phenomenon.

[A]lthough nature-based product limitations are recited by claim 15, analysis of the claim as a whole indicates that claim 15 is focused on a process of detecting the presence of a specific nucleic acid sequence in a sample from a salmon, and is not focused on the nature-based product per se. Id. at 11. For example, as amended herein, claim 15 recites, in part:

a) obtaining a nucleic acid sample from a salmon; and

b) assaying the nucleic acid sample to detect a presence of one or more alleles in the nucleic acid sample;

c) detecting the presence of a cytosine at position 36 in SEQ ID NO: 14.

In response the applicant amended the claims and presented two arguments:

  1. Under the first prong of the Alice test, the applicant argued that the claims were not directed to a natural phenomenon. Specifically, the applicant pointed out that the process of obtaining a DNA sample from the fish, sequencing it, and looking for a particular gene was an artificial process even though it worked on a naturally occurring molecule. As stated by the applicant, the claims were focused on the process of detecting the naturally occurring product and not the naturally occurring product per se.
  2. Under the second prong of the Alice test, the applicant argued that the claims were not merely directed to detecting the naturally occurring product. Instead, the results of the process were used to guide the selective breeding of the fish tested so that the desired characteristic was passed to the offspring. Thus, the claims recited “substantially more” than the process of detecting the naturally occurring product. Specifically, the test results had a real-world use in improving fish husbandry.

The examiner allowed the claims. But the examiner did not identify which of these arguments was found persuasive.

The takeaway from this case is that you should always present arguments on both prongs of the Alice test. In this case, while each argument was powerful independently. the applicant took measures to avoid prolonged prosecution, by presenting both sets of arguments in the office action response.

Kudos to Bradley W. Thomas from Shook, Hardy & Bacon LLP for exemplary work in drafting winning office action responses!

Overcoming §101 Rejections in Molecular Biology Cases

Although some patent practitioners might view Chakrabarty as dated, the “made by man” phrase remains one of the most powerful arguments you have to secure allowance of artificially-created biological inventions.

But you should not limit yourself to “hand of man” arguments. The chances for allowance increase as you present more ways that the claimed molecule differs from its natural counterparts. Look for specific differences in structure and behavior between the claimed molecule and naturally occurring molecules and recite these differences in the claims.

Finally, do not ignore the second prong of the Alice test. Even if you feel optimistic about your arguments that the claims do not embody a natural phenomenon or a product of nature, an examiner might disagree. As a result, you should also present arguments that the claimed invention includes substantially more than a natural phenomenon or product of nature. You can do this by reciting in the claims a real-world application for the invention.

These arguments were found using Arguminer. Visit IP Toolworks to learn more about using Arguminer to find proven arguments for your office action responses.

Disclaimer – “The statements and views expressed in this posting are my own and do not reflect those of my law firm, are intended for general informational purposes only, and do not constitute legal advice or a legal opinion.”

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