DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Applicant's election with traverse of Invention I in the reply filed on June 2, 2026 is acknowledged. The traversal is on the ground(s) that amended claims 1 and 10 are overlapping in scope and mutually inclusive falling under single inventive concept. The response summarizes teaches in the specification. The Applicants argue that based on these teachings the
inventions as claimed in the amended claims 1-9 and 10 share the same or corresponding technical features and are obvious variants of each other and fall under single inventive concept of risk assessment of autism spectrum disorder in a subject.
`These arguments have been fully considered but are not persuasive. In view of the recitation of “corresponding technical features” and “inventive concept” in the response, the Applicants seem to be arguing the “Unity of invention” standard which only applies to application filed under 35 USC 371. However the instant Application was filed under 35 USC 111(a), and therefore the “independent and distinct” standard applies for restriction. The test for distinctness between related products or between related processes evaluates whether the inventions overlap in scope (are mutually exclusive) and whether the inventions are obvious variants. However the instant Inventions are related as product and process of use. In this case, the inventions can be shown to be distinct if either or both of the following can be shown: (1) the process for using the product as claimed can be practiced with another materially different product or (2) the product as claimed can be used in a materially different process of using that product. See MPEP § 806.05(h). In the instant case the method can be practiced with a materially different product. For example the process could be performed using any commercial Real Time PCR machine. Further the claimed product which is merely a medium, a carrier, a processor, and a display device could be used in other processes such as a method of diagnosing periodontal disease. The requirement is still deemed proper and is therefore made FINAL.
Claims 1-10 are currently pending.
Claim 10 is withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on June 2, 2026.
Nucleotide and/or Amino Acid Sequence Disclosures
3. Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). See pages 21-42 of the Specification.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Rejections - 35 USC § 101
4. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-9 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims recite a judicial exception that is not integrated into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The claim analysis is set forth below.
Step 1: The claims are directed to the statutory category of a process.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
The instant claims recite abstract ideas.
The instant claims recite steps that are carried out “via one or more hardware processors”. The processor is recited at a high level of generality. It reads on a generic processor performing generic computer functions of processing data. MPEP 2106.04(a)(2)(III)(C) is very clear that a claim that requires a computer may still recite a mental process. The MPEP states the following:
Claims can recite a mental process even if they are claimed as being performed on a computer. The Supreme Court recognized this in Benson, determining that a mathematical algorithm for converting binary coded decimal to pure binary within a computer’s shift register was an abstract idea. The Court concluded that the algorithm could be performed purely mentally even though the claimed procedures “can be carried out in existing computers long in use, no new machinery being necessary.” 409 U.S at 67, 175 USPQ at 675. See also Mortgage Grader, 811 F.3d at 1324, 117 USPQ2d at 1699 (concluding that concept of “anonymous loan shopping” recited in a computer system claim is an abstract idea because it could be “performed by humans without a computer”).
The claims recite a step of “collating” the quantitative abundance of: (i) each of the plurality of predetermined microbes associated with the saliva sample and (ii) each of the plurality of predetermined microbes associated with the dental plaque sample, to obtain a hybrid abundance matrix. The broadest reasonable interpretation of the “collating” step is that it can be performed in the human mind but for the recitation of a generic “processor”. That is, other than reciting “via one or more hardware processors”, nothing in the claim precludes the “collating” step from practically being performed in the human mind. Mental processes are concepts performed in the human mind (including an observation, evaluation, judgement, opinion) and are abstract ideas. For example, but for the “via one or more hardware processors” language, the claim encompasses reading the abundance of the microbes in a laboratory reporting and putting them in order from highest to lowest abundance.
The claims recite a step of “performing” risk assessment of autism spectrum disorder of the subject, based on the model score and a predefined threshold value. The broadest reasonable interpretation of the “performing” step is that it can be performed in the human mind but for the recitation of a generic “processor”. That is, other than reciting “via one or more hardware processors”, nothing in the claim precludes the “performing” step from practically being performed in the human mind. Mental processes are concepts performed in the human mind (including an observation, evaluation, judgement, opinion) and are abstract ideas. For example, but for the “via one or more hardware processors” language, the claim encompasses comparing the model score to a threshold and thinking about the risk based on the comparison.
The claims recite a step of “determining”, via the one or more hardware processors, a model score based on the hybrid abundance matrix, using a pre-determined machine learning (ML) model. Machine learning models are mathematical concepts. Mathematical concepts are considered to be abstract ideas.
The instant claims recite a law of nature.
The claims recite a correlation between a plurality of microbes (those recited in claims 3-5 and 8-9) and the risk of autism spectrum disorder. This type of correlation is a consequence of natural processes, similar to the naturally occurring correlation found to be a law of nature by the Supreme Court in Mayo.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
The claims do NOT recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s). For example, the claims do not practically apply the judicial exception by including one or more additional elements that the courts have stated integrate the exception into a practical application:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
An additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
An additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
An additional element effects a transformation or reduction of a particular article to a different state or thing; and
An additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological
environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
The claims recite steps that are performed via one or more hardware processors. The processors are recited at a high level of generality. They read on a generic processor performing generic computer functions of processing data. This generic limitation is no more than mere instructions to apply the exceptions using a generic computer component. Accordingly this additional limitation does not integrate the abstract ideas into a practical application because it does not impose any meaningful limits on practicing the abstract ideas.
The claims recite steps of: collecting a saliva sample and a dental plaque sample; extracting microbial deoxyribonucleic acid (DNA) sequences from the samples, individually; determining a quantitative abundance of: (i) each of a plurality of predetermined microbes associated with the saliva sample and (ii) each of a plurality of predetermined microbes associated with the dental plaque sample, individually, from respective extracted DNA sequences, using a first set of probes and a second set of probes specific to each of the plurality of predetermined microbes associated with the saliva sample and the dental plaque sample respectively, through a multiplexed quantitative Polymerase Chain Reaction (qPCR) technique. These steps do NOT integrate the judicial exceptions into a practical application because they merely add insignificant extra-solution activity (data gathering) to the judicial exceptions.
The claims also recite a step of displaying, via the one or more hardware processors, the risk assessment of autism spectrum disorder of the subject. Merely presenting the results of a process otherwise unpatentable under section 101 is, however, insufficient to establish eligibility under the statute. See FairWarning IP, LLC v. Iatric Sys., Inc., (Fed. Cir. Oct. 11, 2016) (claim unpatentable despite recitation of the step: "providing notification if [an] event has occurred").
Step 2B: Evaluate Whether the Claim Provides an Inventive Concept
In addition to the judicial exceptions, the claims recite steps that are performed via one or more hardware processors. The processor is recited at a high level of generality. It reads on a generic processor performing generic computer function of processing data. This amounts to no more than mere instructions to apply the exceptions using a generic computer component. This does not provide an inventive concept.
Further the claims do not amount to significantly more because they simply appends well understood, routine, and conventional activities previously known in the art to the judicial exceptions.
For example Choi (Diagnostics 2020 Vol 10, 965) conducted a study to quantitatively compare bacterial profile of patients with different severity of periodontal disease using samples from mouthwash (saliva) and the subgingival area (plaque). Choi teaches that the samples were quantitatively analyzed for 11 target periodontopathic bacteria using multiplex real-time PCR (abstract, sections 2.3-2.4, 3.3).
Further it is noted that the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity.
Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
Claim Rejections - 35 USC § 112
5. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-2 and 4-9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a Written Description rejection.
The claims are drawn to a method for risk assessment of autism spectrum disorder in a subject. The claims require determining the quantitative abundance of a plurality of microbes in a saliva sample and the quantitative abundance of a plurality of microbes in a dental plaque sample and then using a machine learning model to calculate a score that determines the subjects risk of autism spectrum disorder.
In the instant case, the rejected claims do not set forth the microbes that are quantitated in the saliva sample or the dental plaque sample in terms of sufficient relevant identifying characteristics. The claims encompass quantitating a large genus of microbes that have been identified only in terms of their function. Only claims 4 and 8 define specific microbes in salvia samples that are correlated with ASD. Only claims 5 and 9 define specific microbes in dental plaque samples that are correlated with ASD.
The specification provides written description for the following saliva microbes: Mogibacterium, Peptostreptococcus, Eubacterium, Solobacterium, Actinomyces, and Alistipes that can be used for risk assessment of ASD. The specification provides written description for the following dental plaque microbes: Eubacterium, Dialister, Atopobium, Enterococcus, Mogibacterium, and Anaeroglobus that can be used for risk assessment of ASD. The specification does not describe any other species within these claimed genera to show possession of those species.
Regarding the genera of saliva microbes correlated with ADS and dental plaque microbes correlated with ADS, the specification does not describe any structural features of the disclosed microbes that would have been expected to be shared by members of the claimed genera. The specification does not describe any physical and/or chemical characteristics of the disclosed microbes that would be expected to be shared by members of the claimed genera. All members of the genera have the same function, i.e., they are associated with ASD, but no correlation between their structure and this common function is disclosed. The level of knowledge and skill in the art does not allow those skilled in the art to structurally envisage or recognize additional members of the claimed genera. Because the structure of the species within the claimed genera is expected to vary unpredictably from the structure of the microbes disclosed in the specification, the disclosed microbes are not a “representative number” of species within the claimed genera.
Because the disclosed microbes are not representative of the entire claimed genus, and the specification does not disclose structural features shared by members of the genera, the description of the microbes in the specification would not have put the applicant in possession of common structural attributes or features shared by members of the genera that structurally distinguish the members of the genera from non-members of the genera at the time of filing. Thus the description of the microbes in the specification is not sufficient to describe the claimed genera of saliva microbes associated with ASD and dental plaque microbes associated with ASD. Accordingly, the specification does not provide a representative number of species or sufficient common structural features to show that the applicant would have been in possession of the claimed genera as a whole at the time of filing.
6. Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMANDA HANEY whose telephone number is (571)272-8668. The examiner can normally be reached Monday-Friday, 8:15am-4:45pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMANDA HANEY/Primary Examiner, Art Unit 1682
Prosecution Insights