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 .
Response to Previous Communication
In response to the restriction requirement mailed on 06/24/2026, the Applicant’s attorney, Jenna Fortini, elects Group 1 (i.e. Claims 1, 3-5, 7-17, 19-20, 22, 24, 32-35, and 51-54) without traversal which was filed on 08/24/2026.
The examiner acknowledges the amendments to the claims filed on 08/24/2026.
Priority
This application claims priority to provisional application 63/314402 filed on 02/26/2022.
Status of the Claims
Claims 2, 6, 18, 21, 23, 25-31, and 36-50 are canceled.
Claims 1, 3-5, 7-17, 19-20, 22, 24, 32-35, and 51-54 are pending.
Claims 1, 3-5, 7-17, 19-20, 22, 24, 32-35, and 51-54 are examined herein.
Information Disclosure Statement
The IDS appears to contain references not uploaded in the file wrapper. See struck through references on signed IDS. Additionally, a document that references an audio recording was uploaded and not on the IDS.
The specification contains references throughout the document (see paragraphs 148, 151, and 152 for examples) that are not listed on a proper IDS. Unless the references are in the IDS document filed on 06/26/2025 or on the PTO-892 form, the references have not been considered.
Claim Interpretation
Claim 1 recites an “increased recombinogenic line” which is interpreted by the examiner to mean there is increased recombination rate within a region of a chromosome in that line.
Claims 1,5,7-10, and 12 which recite a “low-recombinogenic pericentromeric chromosomal segment” which is interpreted to be closer to the centromere while “higher recombinogenic state” is interpreted to be closer to the telomere.
Claim 14 recites an “increased recombinogenic potential” which is interpreted by the examiner to mean there is increased recombination within a breeding population.
Claim 33 recites the site-specific nuclease (i.e. a protein) is provided to the cell as a polynucleotide (i.e. not a protein). This is interpreted by the examiner to mean the nuclease protein is encoded by the polynucleotide.
Claim Objections
Claim 4 is objected to because the abbreviation “TALEN” is not defined in the claims or Specification and should be included in the claim.
Claim 9 is objected to because the acronym “QTL” should be defined.
Claim 17 is objected to because it references a “first inverted pericentromeric chromosomal segment” and “second pericentromeric chromosomal segment” while independent Claim 14 recites “inverted first/second pericentromeric chromosomal segments”.
Claim 20 is objected to for reciting “first and second pericentromeric inverted chromosomal segments” while independent Claim 14 recites “inverted first/second pericentromeric chromosomal segments”.
Claim 24 has two “the” next to each other.
Claim 35 is objected to because “Agrobacterium” should be “Agrobacterium”.
Appropriate correction is required.
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, 3-5, 7-17, 19-20, 22, 24, 32-35, and 51-54 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as failing to set forth 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.
Claim 1 recites ‘identifying and targeting a low-recombinogenic pericentromeric chromosomal segment”. “Low” is a relative term and could encompass a broad range of a chromosome’s ability to recombine. Does a pericentromeric chromosomal segment have a lower ability to recombine simply because it is closer to the centromere? Is the comparison made in this claim against other regions on the same chromosome or another chromosome in another species? Any combination thereof? Claims 3-5, 7-13, 24, 32-35, and 51-54 inherit this rejection.
Claims 1, 5, 7-10, 12, 14, 16-17, and 19 recite a “pericentromeric chromosomal segment” which could be any distance from the centromere (see paragraphs 198-199 of the specification). It is unclear how close a chromosomal segment has to be for it to be pericentromeric. Claims 3-4,11,13,15, 20, 24, 32-35, and 51-54 inherit this rejection.
Claim 22 recites a “pericentromeric segment” which could be any distance from the centromere (see paragraphs 198-199 of the specification). It is unclear how close a chromosomal segment has to be for it to be pericentromeric.
Claims 7-8 recite “about” which is a relative term and not defined in the specification. Is 25 kb about 50 kb? Is 500kb about 1Mb?
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 Langi, 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.
For Pending Application: 18/000067 (see US 20230203517 A1 and IDS filed on 06/26/2025)
Claims 1, 4-5, 7-9, 11, 13, 22, 32, and 51 are provisionally rejected on the ground of nonstatutory double patenting as being unpatenable over Claims 1 7-9,11, 13-14, 16 and 31-33 of copending application No. 18/000067 (i.e. ‘067). Although the claims at issue are not identical, they are not patentably distinct from each other because the methods encompass steps that are not patentably distinct.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct
claims have not in fact been patented.
Claims 1 and 14 of ‘067 are drawn to a method for inverting a chromosomal segment in a crop plant that utilizes a Cas endonuclease and two guide RNAs to generate an inversion of a chromosomal segment and regenerating a crop plant. This reads on instant Claims 1,4-5, and 22 which are also drawn to inverting chromosomal segments. Dependent claims 7-9,11, 13, 16 and 33 of ‘067 which are directed to inversion chromosomal segment size, composition of QTLs and/or favorable alleles, and plant species and tissue type read upon immediate Claims 7-9, 11, and 13. Additionally, dependent claims 31 and 32 of ‘067 reads upon immediate Claims 32 and 51 as both are directed to providing a Cas endonuclease as a protein and guide RNA is provided to the crop plant cell.
For Pending Application: 18/713877 (see US 20250027097 A and IDS filed on 06/26/2025)
Claims 1, 4-5, 7-9,11,13, 22, 33, and 52 are provisionally rejected on the ground of nonstatutory double patenting as being unpatenable over Claims 1-2, 4-6, 9-10, 13-14, 16-17 and 34 of copending application No. 18/713877 (i.e. ‘877). Although the claims at issue are not identical, they are not patentably distinct from each other because the methods encompass steps that are not patentably distinct.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct
claims have not in fact been patented.
Claims 1 and 13-14 of ‘887 are directed to modifying a chromosome in a crop plant cell by transforming a polynucleotide encoding a break-inducing agent (i.e. Cas polypeptides) which further comprises providing guide RNA and utilizes two genomic target sites and introducing double strand breaks at these sites for translocations and/or inversions, which reads upon immediate Claims 1, 4-5, 22, 33, and 52 that are also directed to using Cas nucleases to induce double stranded breaks at two locations for an inversion or translocations. Limitations from claims 2, 4-6, 9-10, 16-17 and 34 of ‘877 further reads upon immediate Claims 5,7-9,11,13 and 22 as they are directed to regenerating a crop from the transformed cell, inversions (including pericentric inversions), in homologous chromosomes, inversion sizes, crop species and tissue types, in regions with QTLs.
Claim Rejections - 35 USC § 102/103
A rejection under 35 U.S.C. § 102 or § 103 does not require the same analysis as a rejection under 35 U.S.C. § 102 or a rejection under 35 U.S.C. § 103. The rejection is made because the examiner cannot determine whether the prior art composition possesses characteristics that are not recited in the art. The examiner does not have sufficient facts to determine whether the claimed compositions, polynucleotides, polypeptides and organisms are inherently the same as the prior art compositions, polynucleotides, polypeptides and organisms. In addition, the examiner cannot conclude that the claimed subject matter would have been obvious since it cannot be determined whether the claimed and prior art compositions, polynucleotides, polypeptides and organisms differ. Where the prior art product seems to be identical, except that the prior art is silent to a characteristic or property claimed, then the burden shifts to applicants to provide evidence that the prior art would neither anticipate nor render obvious the claimed invention. In re Best, 195 USPQ 430, 433 (CCPA 1977).
Claims 1, 3-5, 7-8, 10, 12-13, 24, 32, 34, 51, and 53 are rejected as being anticipated under 35 U.S.C. § 102(a)(1), or alternatively as being unpatentable under 35 U.S.C. § 103, over Schwartz, Chris, et al. "CRISPR–Cas9-mediated 75.5-Mb inversion in maize." Nature plants 6.12 (2020): 1427-1431 (see IDS filed on 06/26/2025).
Schwartz et al 2020 “demonstrate the application of CRISPR–Cas9 technology to mediate targeted 75.5-Mb pericentric inversion in chromosome 2 in one of the elite maize inbred lines from Corteva Agriscience. This inversion unlocks a large chromosomal region containing substantial genetic variance for recombination, thus providing opportunities for the development of new maize varieties with improved phenotypes” in the abstract. Paragraph 6 on page 1 teaches the inversion was performed using CRISPR -Cas9 Technology to generate double stranded breaks (see figure 2) using particle bombardment and is visualized in the figure 3a below. The method that utilizes site-specific DNA breaks (i.e. double strand breaks) in regions with low-recombinogenic pericentromeric chromosomal segments (i.e. region between F1 and R1 primers in the top chromosome of Figure 3a) is described on page 4 paragraphs 2-7, Fig 2, page 3 paragraph 3 (i.e. Claim 1). This regions with low-recombinogenic pericentromeric chromosomal segments (i.e. region between F1 and R1 primers below in the top chromosome of Figure 3a) is rearranged and positioned closer to a telomere of the chromosomal arm, resulting in the modified chromosomal arm and is capable of increased recombination frequency compared to a control crop plant cell, presumably in meiotic or mitotic cell division, as was described in applicants Figure 2B (see below), paragraph 39 (of the specification) and abstract of Schwartz et al 2020, which were limitations of Claims 1 and 12. This region was also identified and targeted as “it would restore the original order of chromatin and re-open those regions for recombination [i.e. identified and targeted low-recombinogenic pericentromeric chromosomal segment in a chromosomal arm of a crop plant cell] enable the selection of favorable novel allele combinations that would otherwise be unfeasible” (see page 1 paragraph 5). The abstract also recites “this inversion unlocks a large chromosomal region containing substantial genetic variance for recombination” indicating this plant (i.e. corn i.e. crop i.e. Claim 13) is an increased recombinogenic parental line. This inversion is stable and heritable in a progeny population as was described on page 3 paragraph 2 as it recites “To validate transmission and segregation of the newly redesigned chromosome 2, the two T0 regenerants with the confirmed inversion were grown to maturity and crossed with wild-type PH1V5T plants. In agreement with Mendelian segregation, a total of 114 out of 253 T1 progeny plants (45%) were positive for the inversion [i.e. Claim 10; i.e. segregate during cell division i.e. reproduction/meiosis] when analysed by junction quantitative PCR (qPCR)”. Thus, Schwartz et al 2020 anticipates all the limitations of Claim 1. The site-specific DNA breaks are described as being double strand breaks in figure 2 and page 3 paragraphs 1 and 3 while the abstract recites the DNA is cleaved by the CRISPR-Cas9 (i.e. Cas nuclease) and was the limitation of Claim 4. The abstract and Figure 3 teaches the mutation was an inversion (i.e. Claim 5) that is 75.5Mb long (i.e. at least about 50kb and larger than about 1Mb i.e. Claims 7-8). Schwartz et al 2020 teaches “pre-assembled Cas9–guide RNA (gRNA) ribonucleoprotein (RNP) [i.e. site-specific nuclease protein] complexes were delivered into maize immature embryo cells using particle bombardment” on page 1 paragraph 6 (i.e. Claims 32,34,51, and 53). Schwartz et al 2020 also teaches two pericentric inversion was confirmed in two T0 plants which were crossed with wild-type PH1V5T plants on page 2 paragraph 4 to page 3 to paragraph 2 (i.e. two parental lines in a breeding population of Claim 3). These plants would also be recombination compatible (i.e. Claim 3), and the progeny would be fertile and capable of setting seed (i.e. Claim 24) absent evidence to the contrary.
Accordingly, Schwartz et al 2020 anticipated the claimed invention(s) of Claims 1, 3-5, 7-8, 10, 12-13, 24, 32, 34, 51, and 53.
Alternatively, if it is determined that Schwartz et al 2020 does not recite all the compositions and methods of the instant claims, it would have been prima facie obvious to use the teachings of Schwartz et al 2020 to generate a method that produce an increased recombinogenic parental line of a crop plant as it teaches the limitations listed in the independent Claim 1, and many of the dependent claims, are known in the art and have already been used in methods for chromosomal rearrangement which would give one of ordinary skill in the art a reasonable expectation of success. The use of plants with edited chromosomes in breeding populations would also have been prima facie obvious, as this technology has already been identified as being useful for increasing recombination and providing opportunities for developing new varieties with improved phenotypes. The development of improved phenotypes also provides the motivation for why someone would develop such a method.
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 9, 14-17, 19-20, and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Schwartz, Chris, et al. "CRISPR–Cas9-mediated 75.5-Mb inversion in maize." Nature plants 6.12 (2020): 1427-1431 (see IDS filed on 06/26/2025).
Besides teachings the limitations of Claim 1 (described above) Schwartz et al 2020 teaches this technology can be used to modify chromosomes for increased or decreased recombination potential for novel allele combinations. Because this technology can be used to modify the ability of chromosomes to recombine and promote the identification of novel alleles, it would be prima facie obvious to use this technology to generate a method that comprises one or more QTLs or favorable allele associated with an agronomic trait that was previously not associated with such traits due to a low observable recombination frequency (i.e. Claim 9).
Regarding Claims 14-17, 19, and 20. Schwartz et al 2020 teaches two pericentric inversions (in chromosome 2 i.e. homologous chromosomes; i.e. Claim 20) were confirmed in two T0 maize plants (i.e. Claim 15) which were crossed with wild-type PH1V5T plants on page 2 paragraph 4 to page 3 to paragraph 2 (i.e. first and second breeding lines or parental lines in a breeding population of Claim 14). These plants had an inversion where a pericentromeric chromosomal segment of a chromosomal arm was inverted so the pericentromeric chromosomal segment is positioned closer to the telomeric side of the chromosomal arm (i.e. points (a) and (b) of Claim 14). While Schwartz et al 2020 does not explicitly teach the crossing of these lines with each other, this paper recites this chromosome engineering technology can be used to for plant breeding programs meaning it would have been prima facie obvious to cross them (i.e. obtaining breeding pair, crossing them and obtaining progeny with the resulting first and second inverted pericentromeric chromosomal segment; i.e. points (c)-(e) of Claim 14). Because Schwartz et al 2020 demonstrated an inversion that was 75.5-Mb long and recites 18kb inversions and reciprocal translocations have been reported in Arabidopsis in page 1 paragraph 1, it would have been prima facie obvious to use this technology to invert a first and or second pericentromeric chromosomal segment that is at least 50 kb (i.e. Claim 16) or 1Mb (i.e. Claim 17). Additionally, Schwartz et al 2020 teaches a method where inverting the first and second pericentromeric chromosomal segment comprises a double strand break with site-specific nuclease (CRISPR Cas9) (i.e. Claim 19). The choice in number/location of pericentromeric inversion and which chromosome (i.e. homologous chromosome) is a design choice as the criticality of these inversion being in homologous chromosomes has not been demonstrated by the applicant (i.e. Claim 20).
The method of Claim 22 is also made obvious by Schwartz et al 2020 as the method described on page 1 paragraph 6 and Figure 2 teaches the use of a first targeted site-specific break at a chromosomal arm is present at a pericentromeric segment of the chromosomal arm (i.e. position between F1 and R1 primers in the top chromosome in Fig. 3a) and introducing a second targeted site-specific break closer to the telomeric region (i.e. position between primers F2 and R2 near the right telomere in the top chromosome of Fig. 3A) which were the limitations of Claim 22 (a)-(b). Crop plants were obtained containing a chromosomal inversion of the region between these two site-specific breaks where the pericentromeric segment is rearranged closer towards the telomeric region of the chromosomal arm (see page 3 paragraphs 2) and meets the limitations of Claim 22 (c). This paragraph also teaches a method for preparing progeny plants from the crop plant where the progeny plants comprise the pericentromeric segment rearranged towards the telomeric region of the chromosomal arm by crossing to wild-type plant (i.e. Claim 22 (d)). Using the progeny in a crop breeding program is made prima facie obvious as Schwartz et al 2020 teaches chromosomal engineering can be a practical tool for plant breeding programs and the development of new crop varieties with improved phenotypes (i.e. genetic gain; i.e. Claim 22).
It would have been prima facie obvious to use the teachings of Schwartz et al 2020 to generate methods that produce an increased recombinogenic parental line of a crop plant and/or a crop breeding population as well as a method for relocating a pericentromeric segment of a chromosome in a crop plant. Schwartz et al 2020 teaches the limitations listed in the independent claims (i.e. Claims 1, 14 and 22), and many of the dependent claims, are known in the art and have already been used in methods for chromosomal rearrangement which would give one of ordinary skill in the art a reasonable expectation of success. The use of plants with edited chromosomes in breeding populations would also have been prima facie obvious, as this technology has already been identified as being useful for increasing recombination and providing opportunities for developing new varieties with improved phenotypes. The development of improved phenotypes also provides the motivation for why someone would develop such methods.
Claims 11, 33, 35, 52 and 54, are rejected under 35 U.S.C. 103 as being unpatentable over Schwartz, Chris, et al. "CRISPR–Cas9-mediated 75.5-Mb inversion in maize." Nature plants 6.12 (2020): 1427-1431 (see IDS filed on 06/26/2025) as applied to Claims 1 and 4 in view of Zhu, Haocheng, Chao Li, and Caixia Gao. "Applications of CRISPR–Cas in agriculture and plant biotechnology." Nature Reviews Molecular Cell Biology 21.11 (2020): 661-677.
Besides teaching the limitations of Claims 1 and 4 as described above, Schwartz et al 2020 also teaches the method which utilizes Cas nucleases and providing a guide RNA to the crop plant cell (i.e. Claims 52 and 54) as was described on page 1 paragraph 6 and page 4 paragraphs 3-4 and 7.
Schwartz et al 2020 does teach the method for producing an increased recombinogenic parental line of a crop plant from a somatic crop plant cell wherein the site-specific nuclease is provided to the crop plant cell as a polynucleotide or by Agrobacterium-mediated delivery.
Zhu et al 2020 is directed to highlighting the most recent breakthroughs in CRISPR-Cas related plant biotechnologies and includes CRISPR-Cas reagent delivery. Figure 3a of Zhu et al 2020 teaches the direct delivery of CRISPR-Cas (i.e. site-specific nuclease) as a polynucleotide (i.e. plasmid DNA or RNA) and the use of loaded Agrobacterium (i.e. Agrobacterium-mediated delivery) of Claims 33 and 35. Page 9 paragraph 5 also teaches a method called “virus-assisted gene editing” is known in the art where somatic tissue is infiltrated with Agrobacterium where the sgRNA (i.e. guide RNA) is fused to mobile elements and results in 100% edited progeny (i.e. Claim 11). Another method where somatic tissue is transformed to generate edited plants is described on page 9 paragraph 4 and called “De novo meristem induction”. Furthermore, transforming somatic tissue is a design choice and generally known in the art.
It would have been prima facie obvious to combine the teachings of Schwartz et al 2020 and Zhu et al 2020 to generate a method for producing an increased recombinogenic parental line of a crop plant from a somatic cell wherein the site-specific nuclease (i.e. Cas nuclease) is provided to the crop plant cell as a polynucleotide or by Agrobacterium-mediated delivery while also providing guide RNA. These are mere design choices known in the art as the criticality has not been described by the applicant. Because they are known design choices known in the art, one with ordinary skill in the art would have been motivated to try them with a reasonable expectation of success.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GEORGE W MEYER whose telephone number is (571)272-3733. The examiner can normally be reached Monday - Friday 8:00 am- 5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/GEORGE W MEYER/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
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