DETAILED ACTION
Status of the Claims
Claims 14-27 are currently pending and are the subject of this Office Action.
The following Office Action is in response to Applicant’s communication dated 07/10/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn.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 .
Claim Rejections – 35 U.S.C. 102
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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Drmanac et al.
Claims 14-15, 18, and 22-27 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Drmanac et al. (WO 2009/052214 A2, herein “Drmanac”).
Regarding claims 14, 18, and 22, Drmanac discloses a genomic analysis method (e.g., as per the Abstract), comprising:
labeling a polynucleotide at a target sequence by contacting the polynucleotide with a labeling agent to form a labeled polynucleotide (e.g., as per para 0033-0034), the labeling agent comprising:
a binding structure that binds to the target sequence, wherein the binding structure are synthetic oligodeoxynucleotides (e.g., a probe as per para 0085-0086); and a label comprising a detectable moiety (e.g., a fluorophore as per para 0098) that covalently binds to the polynucleotide within or adjacent to the target sequence (e.g., “post-hybridization cross-linking” as per para 0083 and/or “cross-linking agents may be added after target binding to cross-link, i.e. covalently attach, the two strands of the hybridization complex” as per 0169);
linearizing the labeled polynucleotide to provide a linearized sequence-specific labeled polynucleotide (e.g., stretching as per para 0037, and/or 0172-0174);
detecting the label on the linearized sequence-specific labeled polynucleotide and determining a relative position of the target sequence based on the detected label (e.g., as per para 0038 and/or 0078).
Regarding claim 15, Drmanac discloses the above method, wherein the binding structure is a binding sequence having a nucleotide sequence complementary to the target sequence (e.g., as per para 0033-0034).
Regarding claim 23, Drmanac discloses the above method, wherein linearizing the labeled polynucleotide comprises linearizing the labeled polynucleotide in a fluidic channel, on a surface, or through a nanopore (e.g., on a substrate as per the Abstract and/or nanochannel as per para 0051-0054 and/or nanopores as per para 0054-0056).
Regarding claim 24, Drmanac discloses the above method, wherein labeling a polynucleotide comprises contacting the polynucleotide with a plurality of labeling agents wherein the binding structure in each labeling agent of the plurality of labeling agents binds to a different target sequence in the polynucleotide to provide a multi-labeled polynucleotide (e.g., multiple probes as per para 0078).
Regarding claims 25-26, Drmanac discloses the above method, wherein the polynucleotide is genomic DNA (e.g., as per para 0006).
Regarding claim 27, Drmanac discloses the above method, further comprising detecting a relative distance between the labels on the multi-labeled polynucleotide to provide a barcode of the polynucleotide (e.g., as per para 0020 and/or 0078).
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.
Drmanac et al. and Belousov et al.
Claims 14-27 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac et al. (WO 2009/052214 A2, herein “Drmanac”) in view of Belousov et al. (Nucleic Acids Research, 1997, 25(17):3440-3444, herein “Belousov”) as evidenced by Lampe et al. (Nucleic Acids Research, 1997,25(20):4123-4131, herein “Lampe”).
Drmanac is relied on as above, however, Drmanac only discloses in general terms the covalent binding of the labeling agent to the polynucleotide, as detailed above. The reference is silent as to the reactive group being an electrophile selected from mustards or aziridines and wherein the reactive group and the label are bioorthogonal in reactivity, as set forth in claims 16-17 and 19-21.
Note that Drmanac describes alternative ways to decorate the target polynucleotide, including the use of recA invasive probes (e.g., as per para 0035 and 0163-0168).
Belousov discloses the use of recA invasive probes with attached chlorambucil to covalently attach synthetic oligonucleotides to genomic DNA (e.g., as per the Reaction of ODNs with genomic DNA with RecA protein catalysis section on p. 3441), wherein chlorambucil is a nitrogen mustard as taught by Lampe in the Introduction section.
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 covalently attach the probes of Drmanac with the nitrogen mustard as per Belousov. One of ordinary skill in the art would have been motivated to do so since this would reduce probe dissociation during subsequent preparation and positional analysis, especially during stringent washing or flowing conditions, which was an explicit concern of Drmanac (e.g., as per para 0167).
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 Drmanac explicitly discloses the use of recA invasive probes similar to those of Belousov.
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.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684
Prosecution Insights