DETAILED CORRESPONDENCE
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on August 12, 2026 has been entered.
This action is in response to the papers filed August 12, 2026. Currently, claims 1, 3, 5-11, 13-14, 42, 48-53 are pending. Claims 3, 48-50, have been withdrawn as drawn to non-elected subject matter.
All arguments have been thoroughly reviewed but are deemed non-persuasive for the reasons which follow.
Any objections and rejections not reiterated below are hereby withdrawn.
The Improper Markush rejection has been withdrawn in view of the amendments to the claims.
Election/Restrictions
Applicant's election without traverse of ADAMDEC1 and anti-TL1A antibody with CDRs comprising SEQ ID NO: 346-351, Claims 1-17, 42 in the paper filed December 4, 2025 is acknowledged.
Applicant amended Claims 3 and Added 43-48 directed to non-elected genes. These claims have been withdrawn in view of the election.
The requirement is still deemed proper and is therefore made FINAL.
Priority
This application claims priority to
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The Applicant may wish to review their filing receipt and if appropriate contact the Filing Receipt department to resolve the issues with the data on the filing receipt.
Drawings
The drawings are acceptable.
Claim Rejections - 35 USC § 101
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, 5-11, 13-14, 42, 51-53 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based upon consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Question 1
The claimed invention is directed to a process that involves a natural principle and a judicial exception.
Question 2A Prong I
The claims are taken to be directed to an abstract idea, a law of nature and a natural phenomenon.
Claim 1 is directed to “a method of determining a Crohn’s Disease (CD) subtype status in a subject having CD” by measuring expression of a gene, comparing the measured expression levels to a reference profile, and classifying the CD subtype status when the expression level of ADAMDEC1 is at least 2x greater than the reference expression profile and administering to the subject a therapeutically effective amount of an anti-TL1A antibody based on the classification.
Claim 42 is directed to processing or analyzing a biological sample by inputting data into a trained algorithm to generate a classification for a CD subtype and outputting a report and when the classification indicates the biological sample is positive for the CD-PBmu subtype, administering to the subject a therapeutically effective amount of an anti-TL1A antibody based on the classification.
Claim 1 and the claimed dependent thereon are directed to a process that involves the judicial exceptions of an abstract idea (i.e. the abstract steps of “classifying the subjects CD subtype status”) and a law of nature/natural phenomenon (i.e. the natural correlation between the increased level of expression of ADAMDEC1 and CD-PBmu subtype).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Herein, claim 1 involves the patent-ineligible concept of an abstract process. Claim 1 requires performing the step of “classifying the subject as having a CD-PBmu subtype status”. Neither the specification nor the claims set forth a limiting definition for "classifying" and the claims do not set forth how “classifying” is accomplished. As broadly recited the classifying step may be accomplished mentally by thinking about a subject’s gene expression level and assessing whether the subject has CD-PBmu subtype. Thus, the classifying steps constitutes an abstract process idea.
The claims further recites a comparison between the expression level and a reference expression profile that is deemed an abstract idea (see MPEP 2106.04(a)(2)(III)(A); • claims to “comparing BRCA sequences and determining the existence of alterations,” where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014)). The claims are directed to an increase in the level of expression of at least 2-fold and the expression profile of the control.
With respect to Claim 42, the use of a trained algorithm is a mathematical concept. The trained algorithm is a “mathematical calculation” and falls into the “mathematical concepts” grouping of abstract ideas.
A correlation that preexists in the human is an unpatentable phenomenon. The association between expression levels such as elected ADAMDEC1 and CD-PBmu subtype is a law of nature/natural phenomenon. The "determining the CD subtype” and the preamble each tells users of the process to predict CD-PBmu in the sample, amounts to no more than an "instruction to apply the natural law". This determining step is no more than a mental step. Even if the step requires something more such as to verbalize the discovery of the natural law, this mere verbalization is not an application of the law of nature to a new and useful end. The "determining" step does not require the process user to do anything in light of the correlation. The "determining” step fails to provide the “practical assurance” sought by the Prometheus Court that the “process is more than a drafting effort designed to monopolize the law of nature itself.”
Question 2A Prong II
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception. While the claim recites detecting expression of one or more genes, namely elected ADAMDEC1, this is not an integration of the exception into a practical application. Instead, these elements are data gathering required to perform the method.
The claims have been amended to recite administer to the subject a therapeutically effective amount of an anti-TL1A antibody based on the classification but these steps are conditional. The classifying step in step (d) is only “when” the expression level of ADAMDEC1 is at least 2-fold greater than reference expression profile. Thus, if the subject does not have a 2-fold greater expression, the subject will not be classified as having a CD-Pbmu subtype and thus no administration would be provided. Claim 42 is similarly conditional and the treatment is administered only “when” a condition has been met.
Thus, the claim is “directed to” the exception.
Question 2B
The second step of Alice involves determining whether the remaining elements, either in isolation or combination with the other non patent ineligible elements, are sufficient to “’transform the nature of the claim’ into a patent eligible application” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
The claims are not sufficiently defined to provide a method which is significantly more from a statement of a natural principle for at least these reasons:
The claims do not include applying the judicial exception, or by use of, a particular machine. The claims do not tie the steps to a “particular machine" and therefore do not meet the machine or transformation test on these grounds. The use of machines generally does not impose a meaningful limit on claim scope.
The claims also do not add a specific limitation other than what is well-understood, routine and conventional in the field. The measuring expression is mere data gathering step that amounts to extra solution activity to the judicial exception. It merely tells the users of the method to determine the level of expression of genes in a sample without further specification as to how the sample should be analyzed. The claim does not recite a new, innovative method for such determination. The determining step essentially tells users to determine the markers through whatever known processes they wish to use.
The step of determining the expression levels was well known in the art at the time the invention was made. The prior art teaches that expression analysis using commercially available biochips and arrays that comprise the claimed genes. The steps are recited at a high level of generality. The claim merely instructs a scientist to use any expression analysis assay to determine the expression status. The claims do not require the use of any particular non-conventional reagents. When recited at this high level of generality, there is no meaningful limitation that distinguishes this step from well understood, routine and conventional activities engaged in by scientists prior to applicant’s invention and at the time the application was filed.
Additionally, the teachings in the specification demonstrate the well understood, routine, conventional nature of additional elements because it teaches that the additional elements were well known.
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.
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)
For these reasons the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to Arguments
The response traverses the rejection. The response asserts claim 1 has been amended to recite administering to the subject an effective amount of an anti-TL1A antibody-based on the classification. This argument has been considered but is not convincing because the administrating step is conditional on classifying the subject as having a CD-PBmu subtype. The claim encompasses not classifying subjects as having CD-PBmu and thus, not administering the treatment. Claim 42 is similarly conditional and the step of administering is performed only “when” the classification is positive for the CD-PBmu subtype”. Thus, for the reasons above and those already of record, the rejection is maintained.
Claim Rejections - 35 USC § 112- Second Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1, 5-11, 13-14, 42, 51-53 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
Claim 1 has been amended to remove the recitation of “one or more genes” however the claim requires measuring expression levels which is plural. It is unclear what measuring expression levels of ADAMDEC1 encompasses. It is unclear how ADAMDEC1 has more than one expression level. Claim 13 also requires this limitation. Clarification is required.
Claim 1 has been amended to add an administration step of “administering to the subject” because it is unclear which subject is being referred to, the subject in step (a) or the subject in step (d) that has been classified as having a CD-PBmu subtype. It is unclear whether the claim encompasses analyzing a subject and determining the subject does NOT have the CD-PBmu subtype or the claim requires detecting the CD-PBmu subtype. Clarification is required.
Claim 1 has been amended to add a limitation that the administering is “based on the classification” but it is unclear what based on means. It is unclear what basis is required to administer the antibody. The claim is unclear and does not set forth the basis on which the administration occurs.
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Claim Rejections - 35 USC § 112-
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 53 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 53 has been added to require the gene expression product levels comprise expression levels of ADAMDEC1. This limitation does not appear to limit Claim 1 in any way since Claim 1 also requires measuring expression levels of ADAMDEC1 in the biological sample. The claims are identical in scope. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 1, 5-11, 13-14, 42, 51-53 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 12, 14, 17, 19, 28 of copending Application No. 17/334,109 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other. The claims of ‘109 are directed to treating CD by administering to the subject a modulator or antagonist of TNF Superfamily Member 15 (TL1A) where the subject is identified as having CD-PBmu subtype where the expression profile was increased in ADAMDEC1. The instant claims are similarly directed to detecting expression of elected ADAMDEC1 and determining CD status of CD-PBmu. Instant Claim 16 is further directed at treating by administering a therapeutic agent, namely elected anti-TL1A ab.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
The response traverses the rejection. The response argues that the claims of ‘109 are directed to administering a therapeutically effective amount of an anti-TL1A antibody to a subject who has been identified as having the CD-PBmu subtype based on detecting increased expression of at least 15 specified genes. This argument has been reviewed but is not persuasive because ‘109 claims ADAMDEC1 as one of the 15 genes and the instant claims encompass analysis of additional genes by the open claim language. This is further evidenced by the newly added claims to additional genes. Although the response argues that the instant claims are based on expression of a single gene, this statement does not reflect the comprising claim language of the language of non-elected claims 49-50 which demonstrate additional genes are encompassed by the instant claims. Thus, for the reasons above and those already of record, the rejection is maintained.
Conclusion
No claims allowable.
The art made of record and not relied upon is considered pertinent to applicant's disclosure.
Gonsky et al. (Front. Gastroenterol, Vol 2, October 17, 2023) teaches a blood-based transcriptomic signature stratifies severe Crohn’s disease and defines potentially targetable therapeutic pathways. The research provides expression analysis for CD-PBmu subtyping.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
September 15, 2026
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