DETAILED ACTION
Status of the Claims
Claims 1-23 and 25-30 are currently pending.
Claims 1, 5-6, 8, and 10-11 are amended.
Claim 24 has been canceled by Applicant.
Claims 12-23 and 26-30 have been withdrawn as being drawn to non-elected subject matter (see below).
Claims 1-11 and 25 are examined herein.
The following Office Action is in response to Applicant’s communication dated 02/09/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn.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 .
Response to Restriction Requirement
Applicant's election with traverse of Group I (claims 1-11 and 24-25) in the reply filed on 08/14/2025 is acknowledged. The traversal is on the ground(s) that the search and examination of claims of Group II would not constitute a search burden as the claims of Group II depend from the claims of Group I and contain the limitations of Group I. Consequently, the art identified will likely be relevant for both groups as similar limitations are in both groups.
This is not found persuasive because search burden is not an issue herein, since the instant case is a 371 national stage entry of a PCT case, and search burden is only applicable in restriction practice for applications which enter under, for example, 35 U.S.C. 111. See also, MPEP §801, which explicitly states that, “applications entering the National Stage under 35 U.S.C. 371 as a Designated or Elected Office in the U.S. Patent and Trademark Office is covered in Chapter 1800.” Wherein Chapter 1800, and specifically, 1893.03 (d), clearly states that, “Examiners are reminded that unity of invention (not [US] restriction practice pursuant to 37 CFR 1.141 -1.146)) practice is applicable …in national stage applications submitted under 35 U.S.C. 371.” (Emphasis added). Therefore, an argument for rejoining groups on an alleged lack of undue search burden is not persuasive.
Claims 12-23 and 26-30 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected group, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 08/14/2025.
The requirement is still deemed proper and is therefore made FINAL.
New Claim Rejections - 35 USC § 112(a)
Necessitated by Amendments
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 1-11 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(s), at the time the application was filed, had possession of the claimed invention. This rejection concerns “new matter.”
Claim 1 has been amended to include the limitation “(c) adding a label sequence necessary for sequencing to both ends of the fragments from (b) in one step”, however, the disclosure as originally filed does describe, either expressly or inherently, adding label sequences to both termini “in one step”, nor does the specification describe simultaneous labeling of both fragment ends in one reaction, a one-pot labeling reaction, or any other disclosure reasonably conveying possession of the newly added “in one step” limitation.
Claims 2-11 depend from claim 1 and are similarly rejected.
Applicants are reminded, as per 37 C.F.R. 1.121, that no amendment may introduce new matter into the disclosure of an application, and that in accordance with MPEP §2163(II)(A)(3)(b), when filing an amendment an applicant should show support in the original disclosure for new or amended claims.
MPEP §2163(I) states that to satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. MPEP §2163(I)(B) explains the written description matter as it relates to new and amended claims, stating that the written description requirement prevents an applicant from claiming subject matter that was not adequately described in the specification as filed.
MPEP §2163.06(I) notes “If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph - written description requirement. In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981).”
Modified Claim Rejections - 35 USC § 112(b)
Necessitated by Amendments
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.
Claim 25 is 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 25 depends from claim 24, which has been canceled. Accordingly, the metes and bounds of the claim are unascertainable.
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.
Modified Claim Rejections - 35 USC § 102
Necessitated by Amendments
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.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Morris
Claims 1-4, 7, and 9 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Morris (U.S. PGPub 2020/0370128 A1, of record).
Regarding claim 1, Morris discloses a method for preparing a sequencing library, the method comprising fragmenting sample DNA and treating the resulting fragments of the sample DNA with a single-strand-specific nuclease to remove single-stranded moieties from the fragments (e.g., fragmenting with KAPA Frag enzyme and treated with Mung Bean or RecJf nuclease as per [0035-0036]), then adding a label sequence necessary for sequencing to both ends of the fragments in one step (e.g., adapter ligation as per [0037]), wherein the sample DNA is DNA extracted from a living cell, DNA extracted from a frozen cell, or a stored sample of any of the DNAs (e.g., sample DNA may be genomic DNA extracted from cells in FFPE tissue, fresh-frozen sample, or freshly cut curls from a patient as per [0008], [0014], [0017], [0021], and/or Morris claim 4).
Regarding claims 2, 4, and 7, Morris discloses the above method, wherein the single-strand-specific endonuclease is S1 nuclease, Mung Bean nuclease, or RecJf nuclease (e.g., as per [0008], [0014], [0032], and/or [0036]).
Regarding claim 3, Morris discloses the above method, wherein the treating with the single-strand-specific nuclease includes treating the fragments of the sample DNA with a single- strand-specific endonuclease and then further treating the fragments of the sample DNA with a single-strand-specific exonuclease (e.g., exonuclease treatment as per [0016]).
Regarding claim 9, Morris discloses the above method, further comprising subjecting the fragments of the sample DNA treated with the single-strand-specific nuclease to one or more treatments selected from the group consisting of end repair, addition of a base to a terminal, and amplification (e.g., as per [0037]-[0039]).
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Response to Arguments
The 02/09/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
RE: “Morris teaches treating with a single-strand specific nuclease at the same time as the fragmentation and this is not akin to treating after fragmentation as recited in Applicant's claims. Indeed, there is no reference in Morris to treating fragmented DNA with a single-strand specific nuclease after fragmentation” (emphasis in original) and “[t]he single-strand specific nuclease step of Morris is not the same as the claimed step (b) and even if they were the same, which Applicant does not concede, the steps are not ‘arranged or combine in the same way as the recited’ claims.” (from pages 9-10 of the remarks).
In response, it is first noted that wording of para [0036] states that “Alternatively, in some embodiments, the enzymatic fragmentation reaction may be incubated at 30° C., with 0.1 μL, 0.5 μL, 1 μL, 2 μL, or more Mung Bean Nuclease further added to cleave single-stranded DNA regions and basepair mismatches. In yet other embodiments, the enzymatic fragmentation reaction may be incubated at 30° C., with 0.1 μL, 0.5 μL, 1 μL, 2 μL, or more Rec), further added to cleave single-stranded DNA regions and basepair mismatches.” The term “further” reasonably implies and/or is consistent with single-strand-specific nuclease being additionally added to an already fragmented or fragmenting reaction, and therefore reads on the limitations of the claims.
In addition, it is noted that even in cases wherein the fragmenting (e.g., nicking) enzyme and single-strand-specific nuclease are added at the same time (and incubated for minutes to hours as per para [0035]), there will reasonably be some portion of the newly fragmented (e.g., nicked) dsDNA that will then be a substrate for the single-strand-specific nuclease, thus fulfilling the requirement that the nuclease activity be performed on the resulting fragmented DNA, as per the claims. Note that this would still read on the instant claim, since claim 1 uses the transitional phrase "comprising", which is inclusive or open-ended and does not exclude additional, unrecited elements or method steps (such as portions wherein the single-strand-specific nuclease activity acts on the nucleic acid before the fragmenting activity), as stated in MPEP §2111.03.
Therefore, the claims are properly rejected.
Modified Claim Rejections - 35 USC § 103
Necessitated by Amendments
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.
Morris
Claims 1-11 are rejected under 35 U.S.C. 103 as being unpatentable over Morris (U.S. PGPub 2020/0370128 A1, of record).
Morris is relied on as above; however, the reference is silent on the limitations of the specific concentrations of single-strand-specific nuclease as set forth in claims 5-6, 8, and 10-11.
Morris discloses the use of Mung Bean nuclease in quantities of “0.1 µL, 0.5 µL, 1 µL, 2 µL, or more” (e.g., as per [0032] and [0036]), wherein the Mung Bean nuclease concentration is 10 units/µL from New England Biolabs (e.g., as per the Examples), which corresponds to 1 unit, 5 units, 10 units, 20 units, or more of Mung Bean nuclease. Similarly, Morris also discloses the use of RecJf nuclease in amounts of 3 units, 15 units, 30 units, 60 units or more (e.g., as per [0036]). It is noted that the reference is silent regarding the amount of DNA to which the nuclease is being added. However, in accordance with MPEP § 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists. Furthermore, in accordance with MPEP § 2144.05:
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages”).
Therefore, the claimed concentrations are prima facie obvious in light of the amounts of nuclease disclosed in the reference. Further, the reference explicitly states that any of S1, Mung Bean, and/or RecJf nuclease can be used (e.g., as per [0008], [0014], [0032], and/or [0036]).
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Response to Arguments
Applicant does not offer further arguments regarding the above obviousness rejections beyond what was set forth with regard to the 35 U.S.C. § 102 rejection, above. To the extent that Applicant is merely repeating their previous argument, the Examiner contends that those issues were adequately addressed in the above sections, which are incorporated in their entireties herein by reference.
Conclusion
No claims are allowed.
Applicant's amendment necessitated any 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 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 date of this final action.
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.
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, Heather Calamita can be reached on (571)272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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