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 .
Application Status
This action is written in response to applicant’s correspondence received on 10/28/2025. Claims 1-13, 15-20, 22-23 are pending. Claims 8 and 15 have been amended. Claims 14 and 21 have been cancelled. Claims 1-7 have been withdrawn. Claims 22-23 are newly added. Claims 8-13, 15-20, 22-23 are currently under examination.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow. This Office Action is Final.
Priority
Applicant' s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of 35 U.S.C. 112 (pre-AlA). See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 61922012 fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) for one or more claims of this application. The application fails to provide support for the claims under examination since there is no disclosure therein of a barcode adaptor that comprises 1) a unique molecular identifier (UMI) in addition to a “barcode sequence” or 2) an RNA binding site. The 61922012 application discloses the barcode adaptor comprising a cDNA binding site (See e.g., [0029]-[0034]), but not an RNA binding site or a polyT tract. Thus, the 61922012 application contemplates using the barcode adaptors bound to the beads after first strand and/or second strand synthesis of the cDNA. The first evidence of support of beads comprising a UMI and RNA binding sequence is the non-provisional application 14/586857, filed December 30, 2014. As such, the effective filing date for claims 8-20 is December 30,2014.
Additionally, the ‘012 provisional patent application does not appear to contemplate “interrogating the cell for a phenotype prior to sequencing the cDNA molecules, including contacting the cell with a nucleic acid marker,said nucleic acid marker including a nucleic acid linked to a binder, wherein the binder binds to a cell surface protein, wherein the binder comprises a peptide-MHC,” as recited in claims 8 and 15. Such language appears in the effective filing date of the application filed December 30, 2014.
Claim Rejections - 35 USC § 112
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 8-13, 15-20, and 22-23 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 new matter rejection.
Regarding independent claims 8 and 15, these claims have been amended to recite:
“the method further comprises: interrogating the cell for a phenotype prior to sequencing the cDNA molecules, including contacting the cell with a nucleic acid marker, said nucleic acid marker including a nucleic acid linked to a binder, wherein the binder binds to a cell surface protein, wherein the binder comprises a peptide-MHC.”
The Applicant points to Figure 14, paragraphs 76, 176-179, and 617-620 to support the amendment. As an initial matter, paragraphs 617-620 do not appear to exist in the specifications filed of record. Furthermore, paragraphs 176-179 are directed to hydrophilic compartments and methods of attaching polynucleotides to solid support but do not reference “interrogating” or “peptide MHCs.” Paragraph 76 mentions interrogating cells and furthermore refers to Figure 14.
However, the above recited method steps wherein the method comprises interrogating the cell for a phenotype prior to sequencing is not specifically recited within the specification sufficiently to support the claim limitations of the above amendments, as such a method comprising these steps in this order are not presented within the specification. Thus, sufficient support to claim possession of such amendments are not supported by the specification, where furthermore the method including peptide-MHC molecules is purely speculative (Example 24).
Claims 9-13, 116-20, and 22-23 depend from claims 8 and 15 and do not resolve this issue. These claims are therefore also rejected.
Claims 8-13, 15-20, and 22-23 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 U.S.C. 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (Fed. Cir. 1988). Wands states, on page 1404:
Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of these in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.
Nature of the Invention/Breadth of the Claims
Regarding independent claims 8 and 15, these claims are directed to single cell sequencing methods, where both method claims 8 and 15 recite: “wherein the method further comprises: interrogating the cell for a phenotype prior to sequencing the cDNA molecules, including contacting the cell with a nucleic acid marker, said nucleic acid marker including a nucleic acid linked to a binder, wherein the binder binds to a cell surface protein, wherein the binder comprises a peptide-MHC.” Thus, claims 8 and 15 are ultimately drawn to single cell sequencing methods wherein cells have been interrogated using nucleic acid barcoded peptide-MHC molecules (pMHCs). This claim language is problematic as it is known in the art that the identification and sequencing of single cells using DNA barcoded pMHCs is known to have several, unpredictable technical challenges which the Applicant did not address in their specification (see below).
Guidance in the Specification
Regarding the reduction to practice of a method of single cell sequencing where individual barcoded pMHCs are introduced to interrogate specific cells, the Applicant has not reduced such a method to practice and appears to only offer a purely prophetic example of the use of such pMHCs for such sequencing methods. For instance, Example 24 of the specification appears to be the only portion of the specification directed to the use of such pMHCs. Example 24 of the specification states that: “This example describes an embodiment of the invention based on predicted results rather than results actually achieved,” (paragraph 464). Thus, the Applicant has only put forth such a method as those claimed in claims 8 and 15, where no reduction to practice involving barcoded pMHCs has been demonstrated, where individual sequencing could be performed and correlated to “a single cell” as recited. Furthermore, as discussed below, DNA-barcoded pMHCs and their uses in single cell sequencing are known to be unpredictable, with complex technical challenges to overcome in order to use such technology.
State of the Art
Regarding the state-of-the art, it is known in the art that producing reliable data using nucleic acid-barcoded pMHCs to interrogate single cells is challenging. For instance, Nos (https://doi.org/10.64898/2025.12.19.695506, “ITRAP2, a flexible and robust strategy to assign antigen recognition of T-cells in coupled single-cell TCR-pMHC assay,” preprint published 12/23/2025) is an article which focuses on strategies for analyzing and interpreting data generated from single cell TCR peptide-MHC barcoding data (Title, Abstract, and throughout). Nos teaches that:
“SC [single cell] sequencing often includes a high level of dropouts and risk of cross-contamination. Similarly, barcoded pMHC readouts often suffer from significant background noise. These issues complicate the automatic assignment of pMHC recognition to TCR clonotypes. To overcome these challenges, we developed a method for data denoising - Improved T-cell Receptor Antigen Paring 2 (ITRAP2),” (Abstract)
Thus, Nos teaches that single cell sequencing involving barcoded pMHCs suffer from significant background noise making individual TCR clonotypes difficult to distinguish, where furthermore data analysis methods are required in order to overcome such technical challenges (above, Abstract).
Nos teaches that:
“Barcoded pMHC multimers have also been integrated into single-cell capture technologies, allowing pairing with other single-cell modalities, including TCR sequencing, providing an assay for pairing multiple TCR clonotypes with their pMHC recognition in parallel. However, achieving accurate pairing of single cell-derived TCR and pMHC recognition information has proven challenging due to the intrinsic noise from high dropout or multiplets rates and ambient contamination. Moreover, a substantial level of background noise among pMHC-derived barcodes is observed, likely caused by nonspecific cellular binding, making this data type difficult to handle,” (page 2, fourth paragraph).
Thus, Nos teaches that it is known in the art that applying such barcoded pMHC single cell sequencing approaches is known to be technically challenging owing to intrinsic noise and contamination issues, where such issues are compounded by nonspecific cellular binding. Nos teaches that data generated from such studies is difficult to interpret (above).
Nos teaches that:
“Large-scale TCR-pMHC dataset are highly warranted as input to build machine learning tools for pMHC assignment based on TCR sequence knowledge (Jensen and Nielsen 2024; Deleuran and Nielsen 2025; Croce et al. 2024), (Drost et al. 2025; Moris et al. 2021), and to understand similarity signatures observed across TCRs recognizing the same pMHC. It has also been demonstrated that a substantial fraction of pMHC-TCR pairs in the public domain are false, especially coming from single cell TCR-pMHC datasets (Messemaker et al. 2025). Such observations call for better and statistically robust strategies for TCR-pMHC assignment,” (page 2, fifth paragraph).
Thus, Nos teaches that data generated from single cell pMHC-TCR are known to be false and therefore teaches unpredictability and uncertainty with respect to a practitioner using such technology. Nos further teaches that, as a result of such unpredictability and unreliability, better analysis tools are required to refine single cell datasets which rely on input from single cell TCR-pMHC approaches.
Nos teaches that:
“Several tools have been proposed to handle these challenges and “denoise” coupled single-cell TCR-seq with barcoded pMHC multimers data including ICON (Zhang et al. 2021) and ITRAP 79 (hereafter referred to as ITRAP1) (Povlsen et al. 2023). However, while demonstrating promising performance, they both suffer from important shortcomings. For instance, ICON is dependent on internal negative controls used for signal normalization, and ITRAP1 is reliant on internally defined true positives used to define selection thresholds resulting for instance in an inability to identify cross-reactive TCRs,” (page 2, final paragraph into page 3 first paragraph).
Thus, Nos teaches in total that there are still known technical challenges when implementing pMHC-barcoded single cell sequencing strategies, where much of the data is unreliable, where furthermore new tools and analytical methods are required in order to reliably use such barcoded pMHCs in the context of single cell sequencing (above).
Undue Experimentation
With regards to the undue experimentation, the filed of synthetic pMHCs presents unique challenges to a practitioner attempting to practice such a method. For instance, Zhang (Zhang SQ et al. Nat Biotechnol. 2018 Nov 12:10.1038/nbt.4282) is a research article focused on high-throughput determination of the antigen specificities of T cell receptors in single cells (Title, Abstract, and throughout). Zhang teaches that:
“DNA-barcoded pMHC dextramer technology has been used for the analysis of antigen-binding T cell frequencies to samples of more than 1,000 pMHCs for T cells sorted in bulk. However, with bulk analysis, information on the binding of single or multiple peptides to individual T cells is lost. In addition, antigen-linked TCR sequences cannot be obtained, which is valuable for tracking antigen-binding T cell lineages in disease settings, TCR-based therapeutics development, and for uncovering patterns in TCR-antigen recognition. Another limitation is the high-cost and long-duration associated with synthesizing peptides chemically, which prevents the quick generation of a pMHC library that can be tailored to specific pathogens or neo-antigens in an individual,” (page 2, second paragraph).
Thus, Zhang, similar to Nos, teaches that such DNA-barcoded pMHC technologies suffer from intrinsic challenges when used as single-cell sequencing technologies. Furthermore, as quoted above, Zhang also teaches that the generation of such barcoded pMHC libraries is limiting in that the generation of such molecules comes with a high-cost and also takes a long time (page 2, second paragraph). Thus, a practitioner would not only face inherent technical challenges when implementing such nucleic acid-barcoded pMHC single cell methods – challenges which require unique and innovative solutions to resolve not envisioned by the Applicant (as taught by Nos and Zhang) – the methods also require expensive reagents which are time-consuming to make to be used. Such technological limitations and constraints place undue experimental burden on the practitioner.
In summary, the Applicant has offered only a prophetic example of the reduction to practice of such barcoded pMHCs to be used in single cell sequencing methods, where furthermore such methods appear to comprise inherent technical challenges such as inaccuracy and high background noise (above), where a practitioner is not enabled to practice such a method based only on one prophetic example in the specification. Furthermore, the practitioner would be burdened with designing each barcode/pMHC pairing as well as devising methods to accurately interpret and use the data generated by such a method. The specification is therefore not enabling for the independent claims.
Claims 9-13, 16-20, 22-23 ultimately depend from either independent claims 8 or 15 and do not resolve these 112(a) enablement issues. These claims are therefore also rejected.
Furthermore, regarding claims 22-23, these claims recite the additional limitations of “identifying different B cells or different T cells based on sequencing the nucleic acid marker cDNA molecules including the barcode sequences.” As discussed above, the identification of individual B/T cells using such methods is inherently challenging, as such single cell cloning methods using DNA-barcoded pMHCs specifically generate sufficient noise making individual clonal identification difficult. The Applicant was therefore furthermore not in possession of the limitations of claims 22-23.
Response to Arguments
The Applicant’s arguments have been considered but are not persuasive to place the claims in condition for allowance. The Applicant argues that the new limitations recited in the claims obviate the original art rejections. This argument in itself is not persuasive to place the claims in condition for allowance because recitation of these new limitations prompted additional consideration which required the new 112(a) enablement rejection outlined above.
Double Patenting
The Applicant argues that the argument over double patenting sited patents US 9580736, US 10316345, and US 11098304 is moot in light of the amendments. This argument is persuasive, as the previously recited patents do not appear to claim peptide-MHC conjugated nucleic acid barcodes.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 nonprovisional extension fee (37 CFR 1.17(a)) 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 DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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/D.C.R./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635