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 .
This communication is Final Office Action in response to amendment and remarks filed on 11/26/2025. Claims 1-20 have been examined and are pending.
Response to Amendment
The amendment filed on 11/26/2025 cancelled no claim. No claims were previously cancelled. No new claims are added. Claim 13 was recited as “Currently Amended” but there is no amendment. Therefore, claims 1-20 are pending and addressed below.
Applicant’s amendments made to claim 1, 7, 13, 19 and arguments filed on 11/26/2025 are sufficient to overcome the 101 rejections, set forth in the previous office action. Therefore, Examiner withdraws rejections on claims 1-20 under 35U.S.C.101.
Claim Objections
Claim 13 is objected to because of the following informalities:
Claim 13 recites a status identifier as” Currently Amended”, however there is no amendment made to the claim. Appropriate correction/clarification and proper status identifier are required.
Response to Arguments
Regarding the 101 rejections, the argument has been fully considered and is persuasive.
The rejections are withdrawn because the claims integrate the abstract idea into practical application.
Claims 1-20 are eligible under 35 USC 101.
After reviewing the Applicant’s disclosure and the instant amended claim 1, 7, 13, 19 recites the specifics of encoding a subset of CDR3 sequences from the reference
TCR-seq dataset into numeric vectors which are converted to coordinates in a high-dimensional space. The coordinates are grouped together and the CDR3 sequences are filtered in the pre-clusters, to overcome Alice 101 rejection. As such, the claim qualifies as eligible subject matter under 35 U.S.C. 101.
It is clear to the Examiner that the steps being performed go beyond the limitations and simple implementation of an abstract idea. The claimed invention integrates the judicial exception into a practical application and results in improving computational efficiency for T-cell receptor comparisons.
As such, the claims go far beyond mental processes and methods of organizing human activity or performed in the human mind and are directed to computer-centric immune-repertoire based disease diagnosis problems and solutions.
Applicant’s Specification [0127, 0140, 0159, 0186] notes the specific techniques are not well-understood, routine, and conventional, and thus improves the relevant existing technology in the immune-repertoire based disease diagnosis technology.
Therefore, based on these findings of fact, the Examiner understands the claimed subject matter to be patent eligible. The claimed subject matter satisfies the following: improvements to the functioning of a computer or to any other technology or technical field (see MPEP 2106.05(a)), and/or applying or using 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 (see MPEP 2106.05(e) and Vanda memo).
Allowable Subject Matter
As to the prior art rejections, in interpreting the amended claims, in light of the specification, upon further search and consideration, and for the reasons presented by the amended claims, the Examiner finds the claimed invention to be patentably distinct from the prior art of records. It is found that claim 1-20 is allowable subject to outstanding claim objection. Proper status identifier for each claim is required.
Independent claims 1, 7, 13, and 19, as a whole recite a combination of limitations that has Not been found as define over prior art of record (the combination of Li, (WO 2020/197820 A1), Lu et al. (US 2023/0349914), Zhang et al. (US 2021/0335447), Soilleux et al. (US 2020/0357487), Quake et al. (US 2021/0002722), Zhang et al. (US 2018/0201991), and
NPL1, Joshi, K., de Massy, M.R., Ismail, M. et al. Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer. Nat Med 25, 1549–1559 (2019). https://doi.org/10.1038/s41591-019-0592-2.
NPL2, Gielis S, Moris P, Bittremieux W, De Neuter N, Ogunjimi B, Laukens K, Meysman P. Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires. Front Immunol. 2019 Nov 29;10:2820. doi: 10.3389/fimmu.2019.02820. PMID: 31849987; PMCID: PMC6896208.
NPL3, Redmond D, Poran A, Elemento O. Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med. 2016 Jul 27;8(1):80. doi: 10.1186/s13073-016-0335-7. PMID: 27460926; PMCID: PMC4962388.
NPL4, SPRINGERETAL."PredictionofSpecificTCR-PeptideBindingFromLargeDictionariesOfTCR-PeptidePairs"1-10. Frontier sin Immunology, vol.11, Article1803.Online.25August2020; [retrieved29December2021].Retrieved from the Internet:;DOI:10.3389/fimmu.2020.01803., and
other references.
As allowable subject matter has been indicated, applicant's reply must either comply with all formal requirements or specifically traverse each requirement not complied with, and pending remedy to outstanding issues cited above. See 37 CFR 1.111(b) and MPEP § 707.07(a).
The prior art made of record and relied upon is considered pertinent to applicant’s disclosure.
Zhang et al. (US 2018/0201991),
Klinger et al. (US 2015/0275296, 2018/0355429),
Hause et al. (US 2020/0292526),
Pogorelyy et al. (US 2021/0043276),
Fanham et al. (US 2014/0356339, 2028/0080090),
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SUN M LI whose telephone number is (571)270-5489. Fax is 571-270-6489. The examiner can normally be reached on Mon-Thurs, 8:30am--5pm
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Kambiz Abdi, can be reached on 571-270-6702. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SUN M LI/
Primary Examiner, Art Unit 3685