DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Status of the Application
Claims 1-10 are pending and under examination
The following Office Action is in response to Applicant's communication dated 10/05/2023.
Claim Rejections - 35 USC § 112(b)
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(s) 8 and 9 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 8 and 9 recite “said restriction enzyme used to generate” different fragment sets (i.e. the claims seems to require at least two different restriction enzymes), but the parent claim only recites “said restriction enzyme” singularly and do not introduce multiple separate restriction enzymes for first, second, third, and fourth fragmentation steps. It is unclear if the claim requires one or plurality of different restriction enzymes, hence the scope of protection, the metes and bounds of the claim are unascertainable.
For purposes of examination only, and to facilitate a complete analysis of the claim, the Examiner interprets Claims 9 and 10 to require multiple different restriction enzymes. This interpretation is adopted solely for examination and does not resolve the lack of clarity in the claim language.
Claim Rejections - 35 USC § 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 (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 the appropriate paragraphs of pre-AIA 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 –
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claim(s) 1-7 rejected under pre-AIA 35 U.S.C. 102(b) based upon a public use or sale of the invention. Drmanac et al. (US20110033854A1, Published Feb 10th 2011, disclosed in IDS).
Regarding claim 1, Drmanac discloses a method comprising: a. providing a target polynucleotide; (e.g. nucleic acids are acquired from organism, where in nucleic acid may be DNA, both genomic and cDNA, RNA or a hybrid [¶0052])
b. fragmenting said target polynucleotide to generate a plurality of non-overlapping first polynucleotide fragments; (e.g. “non-overlapping first polynucleotide fragments” is interpreted, consistent with Applicant’s specification, to encompass fragments generated in controlled manner using restriction enzymes [Applicant’s specification ¶0187]. The reference discloses method of fragmentation referred to herein as Controlled Random Enzymatic (CoRE) fragmentation. The CoRE fragmentation methods can be used alone or in combination with other mechanical and enzymatic fragmentation methods [¶0071]. Further, an example of enzymatic fragmentation is restriction endonucleases [¶0090]).
c. partitioning said first polynucleotide fragments to generate partitioned first polynucleotide fragments, wherein at least one partition of said partitioned first polynucleotide fragments comprises a first polynucleotide fragment with a unique sequence within said at least one partition; (e.g. nucleic acid fragments may be physically separated into different aliquots such that the probability of any given region of the genome of both the maternal and paternal component in the same aliquot is very rare. [¶0050]).
d. fragmenting said partitioned first polynucleotide fragments to generate a plurality of non-overlapping second polynucleotide fragments.(e.g. the fragment in each aliquot can be further fragmented to generate shorter fragments using same and/or different fragmenting methods [¶0221]).
Regarding claim 2, the claim is interpreted as a second parallel fragmentation and partitioning workflow performed on the same target polynucleotide as claim 1 (rather than downstream processing after step d of claim 1), resulting in additional set of target derived fragments. Since steps a-c of claim 2 are analogous steps b-d of claim 1, the disclosure recited above for claim 1 steps b-d is relied on for corresponding fragmentation, partitioning, and further fragmentation limitations of claim 2. Additionally, Drmanac discloses isolated genomic DNA divided into separate aliquots for separate parallel fragmentations [0220].
Regarding claim 3 and 4, since claim 1 and claim 2 are interpreted as parallel fragmentation/partitioning workflows performed on the same target polynucleotide sample, the first/second fragments and the third/fourth fragments are generated from the same target. One of ordinary skill in the art would have understood that the resulting fragment sets would share target sequence regions. Hence, Drmanac discloses third polynucleotide fragments overlap with said first polynucleotide fragments and fourth polynucleotide fragments overlap with said second polynucleotide fragments.
Regarding claim 5, Drmanac further discloses target polynucleotide is selected from the group consisting of DNA, RNA, and cDNA. [¶0052]
Regarding claim 6 and 7, Drmanac further discloses first, second, third, and fourth polynucleotide fragments are generated by an enzyme. (e.g. The reference discloses method of fragmentation referred to herein as Controlled Random Enzymatic (CoRE) fragmentation. The CoRE fragmentation methods can be used alone or in combination with other mechanical and enzymatic fragmentation methods [¶0071]. Further, an example of enzymatic fragmentation is restriction endonucleases [¶0090]).
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim 8-10 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Drmanac et al. (US20110033854A1, Published Feb 10th 2011, disclosed in IDS) in view of Makarov et al. (US6777187B2, Published April 3rd 2003).
Regarding claims 8 and 9, Drmanac does not discloses fragmentation restriction enzymes are different across parallel assays.
Makarov discloses preparing multiple sub-libraries from the same DNA by partitioning DNA and digesting the DNA with different restriction endonucleases including 6-base specificity as, for example, BamH I, EcoR I, Hind III, etc.. Makarov further teaches using different restriction digests provide different fragment sets and improved coverage [column 25, lines 26-67].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to apply Makarov’s multiple restriction digest approach to Drmanac’s fragmentation workflow. Drmanac teaches that overlapping genomic fragments between assays are useful for ordering reads, bridging difficult genomic regions, improving assembly, and generating longer contiguous segments [¶0270 and ¶0384]. Makarov teaches generating different fragment sets from the same DNA by digesting samples with different restriction enzymes. Knowing the importance of overlapping sequence fragments from Makarov disclosure, one of ordinary skill in the art would have been motivated to use different restriction enzymes in the parallel workflow to generate shifted overlapping fragment sets from the same target polynucleotide, thus, improving sequence coverage and assembly.
Regarding claim 10, Makarov further discloses digesting the DNA with different restriction endonucleases including 6-base specificity as, for example, BamH I, EcoR I, Hind III, etc.[column 25, lines 43].
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
US 9,567,631 B2
Claim(s) 1-10 rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1-10 of U.S. Patent No. 9567631B2 (the ‘631 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding present claim(s) 1, the claim of the ‘631 patent discloses a method comprising: a. providing a target polynucleotide; b. fragmenting said target polynucleotide to generate a plurality of non-overlapping first polynucleotide fragments; c. partitioning said first polynucleotide fragments to generate partitioned first polynucleotide fragments, wherein at least one partition of said partitioned first polynucleotide fragments comprises a first polynucleotide fragment with a unique sequence within said at least one partition; and d. fragmenting said partitioned first polynucleotide fragments to generate a plurality of non-overlapping second polynucleotide fragments. (e.g. as per claim(s) 1 of the ‘631 patent).
Regarding present claim(s) 2, the claim of the ‘631 patent discloses the method further comprising: a. fragmenting said target polynucleotide to generate a plurality of non-overlapping third polynucleotide fragments; b. partitioning said third polynucleotide fragments to generate partitioned third polynucleotide fragments, wherein at least one partition of said partitioned third polynucleotide fragments comprises a third polynucleotide fragment with a unique sequence within said at least one partition; and c. fragmenting said partitioned third polynucleotide fragments to generate a plurality of non-overlapping fourth polynucleotide fragments. (e.g. as per claim(s) 2 of the ‘631 patent).
Regarding present claim(s) 3, the claim of the ‘631 patent discloses third polynucleotide fragments overlap with said first polynucleotide fragments. (e.g. as per claim(s) 3 of the ‘631 patent).
Regarding present claim(s) 4, the claim of the ‘631 patent discloses fourth polynucleotide fragments overlap with said second polynucleotide fragments. (e.g. as per claim(s) 4 of the ‘631 patent).
Regarding present claim(s) 5, the claim of the ‘631 patent discloses target polynucleotide is selected from the group consisting of DNA, RNA, and cDNA. (e.g. as per claim(s) 5 of the ‘631 patent).
Regarding present claim(s) 6, the claim of the ‘631 patent discloses at least one of said first, second, third, and fourth polynucleotide fragments are generated by an enzyme. (e.g. as per claim(s) 6 of the ‘631 patent).
Regarding present claim(s) 7, the claim of the ‘631 patent discloses enzyme is a restriction enzyme. (e.g. as per claim(s) 7 of the ‘631 patent).
Regarding present claim(s) 8, the claim of the ‘631 patent discloses restriction enzyme used to generate said first polynucleotide fragments is different from said restriction enzyme used to generate said third polynucleotide fragments. (e.g. as per claim(s) 8 of the ‘631 patent).
Regarding present claim(s) 9, the claim of the ‘631 patent discloses restriction enzyme used to generate said second polynucleotide fragments is different from said restriction enzyme used to generate said fourth polynucleotide fragments. (e.g. as per claim(s) 9 of the ‘631 patent).
Regarding present claim(s) 10, the claim of the ‘631 patent discloses restriction enzyme has a recognition site of at least about six nucleotides in length. (e.g. as per claim(s) 10 of the ‘631 patent).
18/386,354
Claim(s)1-4 and 6-7 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 68, 69, 71 72, and 77 of U.S. ApplicationNo. 18/386,354 (the ‘354 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding present claim(s) 1, the claim of the ‘354 application discloses a method comprising: a. providing a target polynucleotide; b. fragmenting said target polynucleotide to generate a plurality of non-overlapping first polynucleotide fragments; c. partitioning said first polynucleotide fragments to generate partitioned first polynucleotide fragments, wherein at least one partition of said partitioned first polynucleotide fragments comprises a first polynucleotide fragment with a unique sequence within said at least one partition; and d. fragmenting said partitioned first polynucleotide fragments to generate a plurality of non-overlapping second polynucleotide fragments. (e.g. as per claim(s) 68 of the ‘354 application).
Regarding present claim(s) 2, the claim of the ‘354 application discloses the method further comprising: a. fragmenting said target polynucleotide to generate a plurality of non-overlapping third polynucleotide fragments; b. partitioning said third polynucleotide fragments to generate partitioned third polynucleotide fragments, wherein at least one partition of said partitioned third polynucleotide fragments comprises a third polynucleotide fragment with a unique sequence within said at least one partition; and c. fragmenting said partitioned third polynucleotide fragments to generate a plurality of non-overlapping fourth polynucleotide fragments. (e.g. as per claim(s) 69 of the ‘354 application).
Regarding present claim(s) 3, the claim of the ‘354 application discloses third polynucleotide fragments overlap with said first polynucleotide fragments. (e.g. as per claim(s) 71 of the ‘354 application).
Regarding present claim(s) 4, the claim of the ‘354 application discloses fourth polynucleotide fragments overlap with said second polynucleotide fragments. (e.g. as per claim(s) 72 of the ‘354 application).
Regarding present claim(s) 6 and 7, the claim of the ‘354 application discloses at least one of said first, second, third, and fourth polynucleotide fragments are generated by restriction enzyme. (e.g. as per claim(s) 77 of the ‘354 application).
Conclusion
No claims are allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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/KHAI QUYNH TIEN PHAM/ Examiner, Art Unit 1684
/JEREMY C FLINDERS/ Primary Examiner, Art Unit 1684
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