DETAILED ACTION
Status of the Claims
Claims 1-4, 8-13, 21-22, 24, 39, 73, 82, 91, and 93-96 are currently pending.
Claims 39, 82, and 91 have been withdrawn as being drawn to non-elected subject matter (see below).
Claims 1-4, 8-13, 21-22, 24, 73, and 93-96 are examined herein.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 10/30/2023, 02/12/2025, and 01/02/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Response to Restriction Requirement
Applicant’s election without traverse of Group I (claims 1-4, 8-13, 21-22, 24, 73, and 93-96) in the reply filed on 05/12/2026 is acknowledged.
Applicant’s election of Group I in the reply filed on 05/12/2026 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)).
Claims 39, 82, and 91 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected groups, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/12/2026.
Claim Rejections - 35 USC § 112(b) -- Indefiniteness
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 21-22 and 93-94 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 21 recites a “first unique molecular identifier (UMI)” on R04 and a “second UMI” on R07, however, claim recites a “first unique molecular identifier (UMI)” on R02 and a “second UMI” on R09. It is unclear if the “first unique molecular identifier (UMI)” on R04 is the same or different from that on R02, and if the “second UMI” on R07 is the same or different from that on R09. Accordingly, the metes and bounds of the claim are unascertainable.
Claim 22 recites that R01 is ligated to a target DNA that is in turn ligated to R05, and that R10 is ligated to the other strand of the target DNA that is in turn ligated to R06, which implies two oligonucleotides. However, claim 1 refers to the complex as being four oligonucleotides, therefore, it is unclear how R01/R02/R03 is a separate oligonucleotide from R04/R05, and how R06/R07 is a separate oligonucleotide from R08/R09/R10 if they are ligated together.
Claims 93 and 94 are drawn to a complex (i.e., they are product claims), but include steps of combining or adding. As per MPEP 2173.05(p), “[a] single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. See In re Katz Interactive Call Processing Patent Litigation, 639 F.3d 1303, 1318, 97 USPQ2d 1737, 1748-49 (Fed. Cir. 2011).”
As per MPEP 2173: It is of utmost importance that patents issue with definite claims that clearly and precisely inform persons skilled in the art of the boundaries of protected subject matter. Therefore, claims that do not meet this standard must be rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph as indefinite. Further, as per MPEP 2173.02: If the language of the claim is such that a person of ordinary skill in the art could not interpret the metes and bounds of the claim so as to understand how to avoid infringement, a rejection of the claim under 35 U.S.C. 112, second paragraph, would be appropriate. As currently written, the metes and bounds of the rejected claims are unascertainable for the reasons set forth above, thus the above claim(s) and all dependent claims are rejected under 35 USC 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph.
Closest Prior Art
The closest prior art is identified as Osborne et al. (U.S. 11,078,482 B2, cited in IDS of 10/30/2023), and in particular the complex of Figs. 3-4 and 7-8. Fig. 3 (in part) depicts the following structure:
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Fig. 8 shows the single example sequence:
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For reference, the complex of instant claim 1 is:
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The main differences between the adaptor of Osborne and of that in the claims are in R02 and R09. Specifically, in the complex of Osborne, the regions corresponding to R02 and R09 are each a single nucleotide (e.g., T and C as per Fig. 8), whereas in the claimed complex (from claim 1), R02 comprises “a single-stranded linker, first unique molecular identifier (UMI), and a first read primer site” and R09 comprises “a single-stranded linker, a second UMI, and a second read primer site.”
The Osborne reference does not disclose the term “unique molecular identifier” or UMI, but does discuss barcodes, including barcodes that “may additionally be used to determine the number of initial target polynucleotide molecules that have been analyzed, i.e., to ‘count’ the number of initial target polynucleotide molecules that have been analyzed. PCR amplification of molecules that have been tagged with a barcode can result in multiple sub-populations of products that are clonally-related in that each of the different sub-populations is amplified from a single tagged molecule” (e.g., as per col. 11). This appears to be functionally equivalent or similar to UMIs. Further, Osborne generally states that barcodes can be located at positions within “[c]ertain polynucleotides described herein” (e.g., as per col. 11-12), but does not disclose or suggest placing them in the position as per the instant claims. Although this might be simply a “design choice” or “obvious to try” as choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success (see MPEP 2143, etc.). In contrast, however, is the location of the “read primer sites” of the present claims (e.g., located in R02 and R09), differs significantly from the corresponding locations in the adaptor of Osborne (e.g., R1 and R2, corresponding to R04 and R07 of the present claims). It would not have been obvious to move the read primer sites of Osborne to arrive at the instantly claimed complex, at least because there is no motivation in the prior art to do so, and since this would reasonably render the prior art unsatisfactory for its intended purpose or change the principle of operation of a reference. Accordingly, the complex of claim 1 and its dependent claims appears to be novel and non-obvious.
Conclusion
Claims 1-4, 8-13, 24, 73, and 95-96 are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684
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