DETAILED ACTION
Status of the Claims
Claims 1-5, 7, 9, and 11-15 are currently pending and are examined herein.
The following Office Action is in response to Applicant’s communication dated 04/28/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Objection to the Abstract
Applicant is reminded of the proper language, content, and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words. It is important that the abstract not exceed 150 words in length since the space provided for the abstract on the computer tape used by the printer is limited. The form and legal phraseology often used in patent claims, such as "means" and "said," should be avoided. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. In certain patents, particularly those for compounds and compositions, wherein the process for making and/or the use thereof are not obvious, the abstract should set forth a process for making and/or use thereof. If the new technical disclosure involves modifications or alternatives, the abstract should mention by way of example the preferred modification or alternative.
The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
Where applicable, the abstract should include the following:
(1) if a machine or apparatus, its organization and operation;
(2) if an article, its method of making;
(3) if a chemical compound, its identity and use;
(4) if a mixture, its ingredients;
(5) if a process, the steps.
The abstract of the disclosure is objected to because it is too short and does not relate enough information about the disclosed invention(s) needed to "…disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details”, as per MPEP 608.01(b). Applicant is instructed to amend the abstract accordingly.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 04/28/2026 is/are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement(s) is/are being considered by the examiner.
Claim Objections
Claim 1 is objected to because of the following informalities: the claim recites “an DNA” in line 17, which should be “a DNA”. Appropriate correction is required.
Claims 13-14 are objected to as being dependent upon a rejected base claim, but would be free from the prior art if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Appropriate correction is required.
Claim Rejections – 35 U.S.C. 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Shendure et al., Church et al., Fodor et al., and Grunenwald et al.
Claims 1-5, 7, 9, 11-12, and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Shendure et al. (U.S. PGPub 2013/0203605 A1) in view of Church et al. (U.S. PGPub 2013/0274117 A1, cited in IDS of 08/02/2022), further in view of Fodor et al. (U.S. PGPub 2011/0160078 A1, cited in IDS of 08/02/2022) and further in view of Grunenwald et al. (U.S. PGPub 2011/0287435 A1).
Regarding claim 1(in part), Shendure discloses a method and kit for the transposase-mediated fragmentation and bead-based capture of genomic DNA (e.g., as per Fig. 1 and/or para 0110 and/or 0169). Church similarly discloses a kit of a plurality of magnetic beads (e.g., beads as per para 0025, which can be magnetic as per para 0052 and/or 0077) each comprising at least 100 DNAs each bead comprising a cellular label (e.g., a 20 nt clonal barcode common to each bead but differing between beads as per para 0024).
However, it is noted that Shendure and Church are silent as to the limitation of molecular labels that differ amongst at least two of the DNAs on a given bead, as set forth in claim 1.
Fodor discloses supports (e.g., such as magnetic beads as per para 0219) which comprise 5-40 nt molecular labels that differ amongst DNAs (e.g., as per para 0121 and/or 0208). Fodor further discloses each bead comprising a common first universal label (e.g., an 18-nt common sequence as per para 0208).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to add the 5-40 nt molecular labels and 18-nt universal sequences of Fodor to the magnetic beads of Shendure and Church. One of ordinary skill in the art would have been motivated to do so since doing so permits different captured molecules to be distinguished and digitally counted (e.g., as per the Abstract of Fodor).
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since adding such labels is outlined by Fodor and comprising relatively basic molecular biology methods and skills, well within the reach of the skilled artisan.
It is further noted that Shendure, Church, and Fodor are silent as to the adaptor DNA oligonucleotide comprising a second universal label that is 10-40 nucleotides in length, is at most 99% identical and can hybridize with a first universal label and an enzyme being a ligase or transposase, as set forth in claim 1, and to the transposome limitations of claims 4-5 and 15.
Similar to Shendure, Grunenwald discloses Tn5 tansposonase-based fragmentation and tagging of DNA but in a transposome complex having a 5’ tag capture domain and a 3’ transposon end (e.g., as per para 0094 and/or 0235-0245, wherein the 5’ tag capture domain, corresponding to the second universal domain, is for hybridizing to the bead-immobilized first universal domain, as per para 0009, 0109, and/or 0152).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to use the Tn5 tansposonase-based fragmentation and tagging of DNA but in a transposome complex having a 5’ tag capture domain and a 3’ transposon end as per Grunenwald in the beads of Shendure/Church and Fodor. One of ordinary skill in the art would have been motivated to do so since such allows for more efficient preparation of sequencing libraries that requires less starting material and no cloning required (e.g., as per para 0017 of Grunenwald).
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since adding such transposome-based library preparation is outlined by Grunenwald and comprises relatively basic molecular biology methods and skills, well within the reach of the skilled artisan.
Regarding claim 7, Church discloses that the magnetic beads are paramagnetic (e.g., as per para 0052).
Regarding claim 9, Church discloses a microwell array comprising at least 96 wells (e.g., as per para 0028).
Regarding claim 11, Church discloses covalent attachment of the DNAs (e.g., as per para 0036 and/or 0053).
Regarding claim 12, Church discloses non-covalent attachment of the DNAs (e.g., as per para 0053-0054 and/or 0080).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEREMY FLINDERS whose telephone number is (571)270-1022. The examiner can normally be reached M-F 10-6:00 EST.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684
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