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 .
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on 8/11/2025 is acknowledged.
Claims 1-3,7-8,13,17,19,23,30,38-41,48-51 are pending. Claims 4-6,9-12,14-16,18,20-22,24-29,31-37,42-47 have been cancelled.
Claims 17,19,23,30,38-41,48-50 are withdrawn as being drawn to a nonelected invention.
An action on the merits for Claims 1-3,7-8,13,51 is set forth below.
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 1-3,7-8,13,51 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.
The claims have been amended to remove the term “Halo” from claim 1. These amendment have been reviewed and are deemed to encompass new matter.
It is noted that throughout the specification the terms barcode and amplification primer are preceded by the term “Halo”. As such the specification describes these terms solely based upon the limitations of the term “Halo”. By the deletion of the term from claim 1, it appears that the claims encompass any type of barcode or amplification primer sequence. However, the specification does provide support for such an embodiment.
Claim Rejections - 35 USC § 112
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 1-3,7-8,13,51 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-3,7-8,13,51 are indefinite over the terms “a reverse second amplification primer sequence” and “a reverse second barcode sequence” . The term “a reverse” is unclear as it is not clear what structure these are the reverse of in the claims. It Is not clear if the reverse sequences are intending to be the reverse of the first amplification primer sequence and the first barcode sequence in the claims or if these structures represent other sequences. Therefore the metes and bounds are unclear.
Claim Rejections - 35 USC § 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 (i.e., changing from AIA to pre-AIA ) 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 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.
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.
Claim(s) 1-2, 7-8 and 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Happe et al. (US Patent 10072260 Sept. 11, 2018).
With regard to claim 1, Happe et al. teaches a probe structure (para 69). Happe et al. teaches a first oligonucleotide with flanking sequences that hybridized to different regions in a fragment target DNA (which can be considered a first target hybridization and a reverse second target hybridization sequence). Happe et al. that multiple barcode sequences can be used (para 69 and 76). Happe et a. teaches multiple primer sequences (para 69 and 74). Happe et al. teaches the strand can be designed 5’ to 3’ (para 70). Happe et al. teaches that the probe can be a completely complementary duplex (para 21, 25). However, Happe et al. does not teach the specific structures in the same order. It would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date to perform a rearrangement of known parts of a structure. The rearrangement of the probe of Happe would be routine optimization of known structures for a polynucleotide probe that comprises the same structural components.
With regard to claim 2, Happe et al. teaches that the structure can include a linker (para 33).
With regard to claim 7, Happe et al. teaches a structures a first and second target polynucleotide sequences (para 69). The regard to the limitation “target polynucleotide sequence is known to have more than one allele” is considered any base pair position.
With regard to claim 8, Happe et al. teaches that the probe can target multiple regions of target loci (para 78). Although Happe et al. does not specifically teach the gap size, “about 2” bp in length, would encompass 1 bp which would be encompassed by two distinct target regions.
With regard to claim 13, Happe et al. teaches that the probe can be DNA (Para 5). Happe et al teaches that multiple probes (para 72).
Claim(s) 3 is/are rejected under 35 U.S.C. 103 as being unpatentable over Happe et al. (US Patent 10072260 Sept. 11, 2018) as applied to claims 1-2, 7-8 and 13 in view of Shah et al. (US Patent Application Publication 2020/0165599 May 28, 2020).
Happe et al. teaches a probe structure (para 69). Happe et al. teaches a first oligonucleotide with flanking sequences that hybridized to different regions in a fragment target DNA (which can be considered a first target hybridization and a reverse second target hybridization sequence). Happe et al. that multiple barcode sequences can be used (para 69 and 76). Happe et a. teaches multiple primer sequences (para 69 and 74). Happe et al. teaches the strand can be designed 5’ to 3’ (para 70). Happe et al. teaches that the probe can be a completely complementary duplex (para 21, 25). However, Happe et al. does not teach the specific structures in the same order. It would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date to perform a rearrangement of known parts of a structure. The rearrangement of the probe of Happe would be routine optimization of known structures for a polynucleotide probe that comprises the same structural components.
Happe et al. does not teach a spacer sequence..
With regard to claim 3, Shah et al. teaches that probes can include spacer regions between primer regions (para 94-98). Shah et al. teaches that these can include non-nucleotide spacers and therefore would be considered non-human polynucleotide sequences (para 94-98).
Therefore it would be prima facie obvious to the ordinary artisan at the time of the effective filing date to modify Happe et al. to include the spacer of Shah et al in the probe structure. It would be obvious as spacers a known structures within probes that can be used to space out primer target areas for efficiency (para 94-98). Therefore it would be routine to modify the probe of Happe et al. with known structures of probes with the intended outcome of a probe that can be used for detection.
Claim(s) 51 is/are rejected under 35 U.S.C. 103 as being unpatentable over Happe et al. (US Patent 10072260 Sept. 11, 2018) as applied to claims 1-2, 7-8 and 13 in view of LaBaer et al (US Patent Application Publication 2019/0366237 December 5, 2019)
Happe et al. teaches a probe structure (para 69). Happe et al. teaches a first oligonucleotide with flanking sequences that hybridized to different regions in a fragment target DNA (which can be considered a first target hybridization and a reverse second target hybridization sequence). Happe et al. that multiple barcode sequences can be used (para 69 and 76). Happe et a. teaches multiple primer sequences (para 69 and 74). Happe et al. teaches the strand can be designed 5’ to 3’ (para 70). Happe et al. teaches that the probe can be a completely complementary duplex (para 21, 25). However, Happe et al. does not teach the specific structures in the same order. It would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date to perform a rearrangement of known parts of a structure. The rearrangement of the probe of Happe would be routine optimization of known structures for a polynucleotide probe that comprises the same structural components.
Happe et al. does not teach a tag..
With regard to claim 51, Labear et al. teaches a Halo fusion tag between the barcode and the target of interests (para 23). Labear et al. teaches a florescent tag (para 30) and as such these can be detected digitally.
Therefore it would be prima facie obvious to the ordinary artisan at the time of the effective filing date to modify Happe et al. to include the tag of Labear in the probe structure. It would be obvious as tags are known structures within probes that can be used to label areas of the probe for detection (para 30, 45). Therefore it would be routine to modify the probe of Happe et al. with known tag structures of probes with the intended outcome of a probe that can be used for detection.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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/KATHERINE D SALMON/ Primary Examiner, Art Unit 1682