DETAILED ACTION
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 .
The amendments of 04/23/2026 have been entered in full. Claims 1-17, 19, 20, 23, and 27 are pending.
Election/Restrictions
Applicant’s election of claim 1 in the reply filed on 04/23/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
As noted in the requirement for restriction/election and in Applicant remarks filed on 04/23/2026, the pending claims encompass methods wherein subjects are stratified either by determining the frequency of cell subsets in Table 1, or by expression of genes listed in Table 2 or Table 14. Applicant’s election of claim 1 indicates that embodiments wherein subjects are stratified by determining the frequency of cell subsets in Table 1 are under consideration. Therefore, claims 1-6 and 11-17, 19, 20, 23, and 27 are readable on the elected species, with the exception that the alternative in claim 12 reciting determination of gene expression is non-elected subject matter.
Claims 7-10 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected method, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 04/23/2026.
Claims 1-6 and 11-17, 19, 20, 23, and 27 are under consideration.
Claim Rejections - 35 USC § 112
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 20, 23, and 27 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 20 recites the limitations "cell states or genes"; claims 23 and 27 recite “cell state”; claim 23 recites “parent cells” in claim 1. In each case, there is insufficient antecedent basis for the limitation in the claim.
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 1-6 and 11-17, 19, 20, 23, and 27 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for methods comprising comparing the frequency of cell subsets in subjects suffering from IBD to a control frequency for subjects having functional gastrointestinal disorders (FGID), does not reasonably provide enablement for methods employing other types of controls, such samples from healthy subjects. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
The specification teaches that, in general, methods of predicting disease risk may rely on detecting an altered quantity or phenotype of the cells in the subject compared to a control subject having normal status or not having a disease indicates response to treatment ([0081-0087] in publication US 20240150453). Thus, the term “control”, as used in the claims without further definition, encompasses methods involving samples from healthy subjects, or at least subjects having conditions other than IBD that would justify obtaining an intestinal biopsy.
The claimed invention addresses a perceived need for a treatment-naïve single-cell atlas in an inflammatory disease condition linking observed baseline cell clusters with disease trajectory and treatment outcomes [0177][0230]. The specification teaches that the claimed methods are based on the results of a prospective clinical study of patients requiring a diagnostic biopsy for possible IBD, prior to diagnosis [0230]. This patient population included patients with FGID, which the specification describes as “a tremendously valuable control group” which served as a critical comparator to contextualize the evidence of immune pathology observed in patients with pediCD [0004][0230]. Therefore, the claimed method was developed and validated by making comparisons of samples from subjects in subjects suffering from IBD to a control frequency for subjects having FGID. It is not certain that a comparably useful method could be developed using a different control group, and even if that is possible, such a method is not disclosed in the instant specification.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DANIEL C GAMETT, Ph.D., whose telephone number is (571)272-1853. The examiner can normally be reached on M-W 9:00 am-5:30pm, EST. Please note the examiner’s part-time schedule. 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, Joanne Hama can be reached on 5712722911. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/DANIEL C GAMETT/Primary Examiner
Art Unit 1647
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