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, species OsNramp5, 18bp deletion in the reply filed on 6/9/2025 is acknowledged.
Priority
This application claims benefit to PCT application No. PCT/CN2020/077242, filed on 2/28/2020, in a language other than English.
MPEP 1895.01 states that in this case “A certified copy of the international application (and an English translation of the international application) may be required by the examiner to perfect the claim for benefit under 35 U.S.C. 120 and 365(c) if the international application did not originate in the United States and such is necessary, for example, where an intervening reference is found and applied in a rejection of one or more claims.”
As an intervening reference is applied in this Office action, and as no English translation of the international application has been filed, a certified English translation is required to establish priority.
The effective filing date of the instant claims is the actual filing date of the instant application, namely 6/2/2022.
Additionally, Applicant cannot rely upon the certified copy of the foreign priority application to overcome any prior art rejection in this Office action because a translation of said application has not been made of record in accordance with 37 CFR 1.55. When an English language translation of a non-English language foreign application is required, the translation must be that of the certified copy (of the foreign application as filed) submitted together with a statement that the translation of the certified copy is accurate. See MPEP §§ 215 and 216.
In the response filed 10/11/2025, applicant stated that translations of the foreign priority documents will be filed, but failed to mention filing a translation of the PCT application No. PCT/CN2020/077242, filed on 2/28/2020, in a language other than English. In order to perfect the claim to priority a translation of the parent application will be required as well.
The effective filing date of the instant claims is the actual filing date of the instant application, namely 6/2/2022.
Claim Objections
Claim 10 is objected to because of the following informalities: “each population consist of” should be “each population consists of”. 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 1-4 and 7-15 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.
In claim 1, step (c) the claim recites “such as 96 individual plants.” The phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). Part (d) later refers to sequencing performed “for a population of 96 plants” and this is unclear because it was not clear that a population of 96 plants was previously required, and so it is unclear if this is also exemplary language or if in fact it is required that the populations comprise 96 individual plants, consist of 96 plants or could be smaller than 96 plants.
Claim 1 recites aligning the sequencing result for the target gene region to identify whether the pooled DNA sample comprises “one or more target” SNP or Indel. However, the specification does not teach sequencing at a depth of >5000x to identify “target” SNP or indel; this step is taught in the context of SNP/indel discovery (paragraph 113).
Claim 1, and all claims that depend from it contains the trademark/trade name “KASP” (trademark) and “Kompetitive Allele Specific PCR” (trade name). Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a genotyping verification mode and employed primers and, accordingly, the identification/description is indefinite.
Claim 2 recites that the method “further” comprises verifying the identification of “the target SNP and or Indel” which lacks proper antecedent basis because claim 1 does not require detecting a target SNP or Indel, but instead recites determining “whether” or not one or more target SNP or Indel is present. Furthermore, if the target SNP or Indel is present, claim 1 already requires a verification step using dPCR, and it is not clear how the verification mode recited in Claim 2(i) differs from what is required in Claim 1(e)(i). Likewise for the recitation of allele specific PCR in claim 2, relative to the recitation of allele specific PCR in claim 1(e)(ii). It appears these are duplicative steps and not “further” steps relative to claim 1. It is not clear what “further” is actually required.
Claim 3 recites the method of claim 1, wherein step (g) is followed by a verification process. However, claim 1 does not have a step (g). Furthermore, claim 3 recites a verification process which is very similar (almost identical) to the verification process in claim 1, and it is not clear how claim 3’s verification process is meant to interact with the process recited in claim 1. The steps appear duplicative. Furthermore, the phrase “the identification of the target SNPs and/or INDELS in the sequencing result” which lacks proper antecedent basis. It is unclear if the claim requires identifying a SNP or indel, or if this remains conditional as it is in claim 1.
Claim 4 recites a numerical range without context as to what the numbers refer to. Although the claim states that it is of “a reference genome” the reference genome is undefined and so the numbers are essentially relative numbers that lack context. Numbering in genomes is not consistent from one sequenced version to another.
Claim 8 is indefinite because it recites “the physical and chemical mutagenesis in step a)” but claim 1 has been amended to recite “physical or chemical mutagenesis. Claim 8 is indefinite because it is not clear if the alkylating agent mutagenesis is meant to require all of those listed modalities, or if only one is required. The plain claim language says that the alkylating agent mutagenesis comprises ethyl methanesulfonate (EMS) mutagenesis….and ethyleneimine (EI) mutagenesis” which on its face sets forth that all of these are required, but this is not consistent with the disclosure where only one type of mutagenesis is used at a time.
Claim 10 recites that each population “consist of” 48, 96, or 192 plants, which conflicts with step 1(d)(iv) which recites that sequencing is performed at a depth of at least 5000x for 96 plants. If a population of 96 plants is required in claim 1, it is not clear how that population can consist of 48 plants. Furthermore, since claim 1 requires sequencing at 5000x it is not clear how sequencing for a single population consisting of 48 plants “is greater than 2000x”- which suggests that perhaps sequencing between 2000 and 5000x would meet the limitation but conflicts with claim 1 which is understood to require sequencing at 5000x.
Claim 12 is indefinite because it recites “the target gene is the Oryza sativa OsNramp5 gene” (elected), but claim 1 refers to “a target gene region” and it is not clear if claim 12 intends to require sequencing of “the Oryza sativa OsNramp5 gene” or “the Oryza sativa OsNramp5 gene region.”
Claim 13 is indefinite when it refers “the identified chimeric individual plant” because claim 3 does not require an identified chimeric plant. This is highlighted by the fact that claim 3 part (1) recites “if so, proceeding to step 2” indicating that neither step 2 nor is determining which individual plant is a chimeric individual required. Furthermore, the recitation “leaves corresponding to each ear” is indefinite because the claim does not previously recite or require a plant that has an “ear” so it is not clear what “each ear” refers to.
Claim 13 is indefinite when it refers to “a mutation” because it is unclear how the recited mutation relates to claim 1 which determines “whether” pooled DNA has a SNP or an Indel. First, claim 1 simply requires determining “whether” the SNP or Indel is present, so if it is not present, is claim 13 required? Second is the SNP or Indel the same as “a mutation” as recited in claim 13?
Claim Rejections - 35 USC § 102
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.
Claim(s) 1-4 and 7-8, 10, 12-15 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by CN110904258-A.
The instant application is a continuation of a PCT application which was filed in Chinese, and also claims foreign priority to four Chinese patent applications.
Certified translations of these documents have not been provided.
Therefore, the effective filing date of the current claims is the actual filing date of this application 6/2/2022.
The Chinese reference teaches the claimed invention, see figure 1 and throughout, particularly example 1.
Claim Rejections - 35 USC § 103
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, 3, 8, 10, 13, 14, and 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stuurman (US 8716550) in view of Thys, Schmitt et al. (PNAS, 2012, Vol. 109, No. 36, pages 14508-14513), and Blombery et al. (Arch Pathol Lab Med. 2018;142:606–612; doi: 10.5858/arpa.2017-0229-OA).
Stuurman specifically teaches that an invention “to screen for heritable mutations in any M1 population of plants, directly after seed mutagenesis.” See Col. 2, lines 63-65 and Col. 5, lines 10-17. Stuurman teaches a method for high-throughput targeted identification of an M1 generation plant mutant resulting from physical and chemical mutagenesis, comprising the following steps:
(a) mutagenizing plants by the physical and chemical mutagenesis at a non-lethal dose to obtain M1 generation plant material;
Stuurman teaches providing mutagenizing plant seeds (i.e. plants) by chemical or physical means (Col. 4, lines 24-45). The dose used by Stuurman is “non-lethal” because plants are grown from the mutagenized material.
Stuurman teaches (b) planting each individual plant in the M1 generation plant material independently and growing a plurality of M1 plants. See Col. 3, lines 30-49 and throughout.
Stuurman teaches (c) grouping the M1 generation plants into one or more populations, wherein each population comprises a plurality of individual plants. Stuurman describes tissue sampling of 1440 plants on a grid, then pooling tissue samples according to their coordinate (coordinate corresponds to claimed populations). The reference teaches pools of 160 plants per row, 144 plants per block and 90 plants per column (Col. 10, lines 3-15).
Stuurman teaches for each of the populations (d)(i) collecting leaves from each individual plant and (d)(ii) pooling the collected leaves to form a mixed leaf pool. See Col. 3, line 25 and following, and Col. 10, line 4 and following. The reference teaches (d)(iii) genomic DNA was extracted. See Col. 3, line 36 and Col. 10, line 11.
Stuurman teaches (d)(iv) subjecting the mixed pool of DNA to high-depth targeted sequencing for a target gene region. Stuurman teaches using PCR to amplify the DNA containing the region or gene of interest, see Col. 5, line 56-39, and then sequencing the amplicon using high throughput sequencing methods, which are high depth sequencing methods. See Col. 6, lines 5 and following, and Col. 7, lines 12 and following.
Stuurman teaches (d)(v) aligning a high-depth targeted sequencing result with a related sequence of the target gene region to identify whether a population DNA sample in the high-depth targeted sequencing result comprises single nucleotide polymorphisms and/or Indels of the target gene region. See Col. 6, lines 44 and following.
Step (e) of claim 1 is conditional, and required only if a mutant is identified. As Stuurman teaches embodiments where a pool does not contain a mutant, these steps need not be addressed. See MPEP 2111.04(II): “The broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.”
With regard to claim 8, Stuurman teaches physical and chemical mutagenesis including UV mutagenesis and EMS mutagenesis, among others (Col. 4, lines 24 and following).
With regard to claim 10, Stuurman teaches that the populations of pooled plants included 160 plants, 144 plants or 90 plants (Col. 10, lines 5-15), which was dependent on the size of the N-dimensional grid employed in the method (Col. 4, beginning line 59). Sturrman does not teach pools that consist of 48, 96, or 192 plants, but these numbers are not dislosed as having any criticality. It would have been obvious to optimize the number of plants in a pool according to the desired grid size used.
Stuurman teaches the target gene region comprises an exon region (i.e. protein-coding region) or a non-coding region (Col. 3, lines 58-59); the sequencing can be nanopore sequencing (i.e. a third generation sequencing-based single-molecule targeted sequencing technology); and amplified products are sequenced with sufficient redundancy to make the distinction between sequencing errors and genuine genome sequencing (Col. 7, line 14 and following). This redundancy is a depth sufficient to detect mutations in the population because it is clear from the teaching that the reference is directing to sequence at a depth to allow for identification of a signal.
Stuurman et al. does not teach that the sequencing is performed at a depth of at least 5000X.
Thys teaches that high accuracy can be achieved with ultra-deep sequencing (p. 31, Col. 1 and Table 1) and also that a minimal coverage of 2000x appears to be required in order to ensure an accurate quantitative assessment of minor variant frequencies.
Schmitt et al. teach detection of ultra-rare mutations by next-generation sequencing. The reference teaches a method of sequencing to discover or detect rare mutations which includes sequencing to a 20,000X final depth, and allowed accurate recovery of very rare mutations (p. 14511).
Additionally, prior to the invention, Blombery et al. taught targeted sequencing to a depth of greater than 300,000X (p. 609, first column).
Thys, Schmitt et al., and Blombery demonstrate the detection of low frequency mutations using ultra high-depth sequencing techniques.
Therefore, it would have been obvious to have modified the method taught by Stuurman et al. so as to have employed ultra-deep sequencing at a depth of at least 5000x for the detection of mutants. One would have been motivated to use the ultra-deep sequencing techniques to ensure the accurate assessment of newly mutated alleles in target gene regions. With regard to claims 2, 3, 13, 14, and 15 these claims further define the steps that happen “if’ a mutant is identified. Therefore, although they further limit some conditional embodiments of the claims, they do not require anything further if the condition is not met. Therefore, they do not distinguish from the references.
Claim(s) 4 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Stuurman et al. in view Thys, Schmitt, and Blombery as applied to claims 1, 2, 3, 8, 10, 13, 14, and 15 above, and further in view of Ishiwaka (PNAS, Nov 20, 2012, Vol. 109, No. 47, pages 19166-19171; cited in IDS 7/20/2022).
The teachings Stuurman et al., thys, Schmitt, and Blombery as they address claim 1 are given previously in this Office action and are fully incorporated herein. Stuurman et al. does not teach that the target gene region is a gene sequence of Oryza sativa OsNramp5 gene.
Claim 4 recites “there is an 18 bp deletion” but it does not require detecting the deletion, nor does it clearly require employing the KASP genotyping primers since “the KASP genotyping primer” modifies the KASP genotyping primer which is recited in the conditional part of claim 1.
Ishiwaka teaches that mutations in the O. sativa OsNramp5 gene modulate cadmium rice and can be used in the development of low-cadmium rice. Ishiwaka teaches growing M2 plants which inherently incudes selecting seeds from mutated plants and growing the seeds.
Therefore, it would have been prima facie obvious to have modified the method taught by Stuurman et al. so as to have amplified and sequenced the O. sativa OsNramp5 gene. Stuurman et al. teaches that the advantage of the disclosed approach is that specific mutations can be made in different crops depending on actual needs (Col. 3, line 20), and Ishiwaka teaches that there is a need to provide rice varieties with low cadmium levels. Therefore, one would have been motivated to search for mutants in the OsNramp5 gene of rice plants in order to identify additional, improved rice varieties.
Claim(s) 7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stuurman et al. in view of Thys, Schmitt et al., and Blombery et al., as applied to claims 1, 2, 3, 8, 10, 13, 14, and 15 above, and further in view of Alvarez-Holguin et al. (Rev Mex Cienc Pecu 2019;10(1):227-238).
The teachings Stuurman et al. in view of Thys, Schmitt et al., and Blombery et al. as they address claim 1 are given previously in this Office action and are fully incorporated herein. Stuurman et al. does not teach that the non-lethal dose is within a range of 20% higher or lower than a medial lethal dose. Stuurman teaches that the level of mutagenesis can be within a broad range and can be adapted to achieve whatever range is desired by prolonging the exposure to the mutagenizing means (Col. 4, lines 47-58).
Further, Alvarez-Holguin teaches that the medial lethal dose (LD50) is a parameter utilized to establish the adequate irradiation dose to induce mutations in plant breeding programs and that the highest probability to generate useful mutations for breeding programs occurs at doses where 50% of the irradiated individuals die (p. 2).
Therefore, it would have been obvious to one having ordinary skill in the art before the effective filing date to have employed a median lethal mutagenesis dose in the methods taught by Stuurman et al. One would have been motivated to do so to obtain the highest probability to generate useful mutations for breeding programs, as taught by Alvarez-Holguin.
Response to Remarks
Applicant argues that Stuurman does not teach collecting leaves from different individual plants within a population, pooling them into a single mixed sample, and extracting DNA from that mixed pool. However, this limitation is taught in the reference at least Col. 10, lines 3-15. The reference teaches pools of 160 plants per row, 144 plants per block and 90 plants per column.
Applicant argues that Stuurman does not teach high-depth targeted sequencing. This is addressed in the rejection by providing a combination of references.
Applicant argues that Stuurman does not teach a two-step verification workflow. This is an argument against claim limitations that are not required by the claim since they are set forth as a conditional limitations. Similarly, applicant argues that Sturrman does not teach dPCR and KASP genotyping. These limitations are not required as they only appear in conditional portions of the claims.
The rejections are modified to address the amended claims. New rejections are set forth.
Prior art teachings pertinent to the disclosure but not relied upon herein:
Skadhauge et al. also teaches a method which includes mutagenesis, growing M1 plants, taking pooled samples and identifying a mutation in a gene region of interest (Figure 1 and throughout). Skadhauge et al. teach that once a pool of interest has been identified the methods comprise a step of identifying parts within the pool comprising the mutation of interest (p. 59, line 31). This may be done by testing each progeny for the presence of the mutation (p. 60, line2). Skadhauge et al. teaches digital PCR for the detection of mutations (p. 43 and following).
Rosas teaches KASP is a competitive allele specific PCR for closed-tube SNP genotyping,
based on endpoint detection of allele-specific Förster resonance energy transfer (FRET) fluorescence signals. KASP has low cost, high throughput, and high specificity and sensitivity as has been demonstrated in massive SNP genotyping studies in biomedical research, genome-wide SNP platforms for rice genotyping and molecular markers–assisted wheat breeding.
Karlin-Neumann teaches that “To confirm NGS results, a more targeted and sensitive assay like ddPCR is often used (PDF, p. 2; Karlin-Neumann, 2/19/16, obtained from https://www.americanlaboratory.com/914-Application-Notes/183421-Improved-Liquid-Biopsies-With-Combined-Digital-PCR-and-Next-Generation-Sequencing/#:~:text=When%20initial%20ddPCR%20plasma%20genotyping,like%20ddPCR%20is%20often%20used on 1/8/2016).”
Hindson et al. teach “Thus, once target genes have been identified, greater precision can readily be achieved with ddPCR since the number of reads can be scaled almost arbitrarily. The current ddPCR system can achieve read depths of up to 20 000X for two genes from a single well (p. 8606, 2nd column; Hindson et al. Anal. Chem. 2011, 83, 8604–8610).”
Van Eijk et al. (WO 2007/037678) teach a method which includes pooling genomic DNA from multiple plants, identifying a mutation in the genomic DNA by sequencing, and then amplifying the same pooled library with allele specific primers to detect the mutation p. 7, steps (b), (d), and (j) in particular.
Applicant's amendment necessitated the 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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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, Winston Shen can be reached at (571)-272-3157. 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.
Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/ Primary Examiner, Art Unit 1682
Prosecution Insights