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 .
Application Status
This action is written in response to applicant’s correspondence received 10 December 2025. Claims 1 and 4-20 are currently pending. Claim 8-20 are withdrawn from prosecution as being drawn to non-elected subject matter. Claim 1 is amended. Accordingly, claims 1 and 4-7 are examined herein. The restriction requirement mailed 5 February 2024 is still deemed proper. Applicant's elected Group I, claims 1-7, without traverse in the reply filed 5 April 2024.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
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 and 4-7 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.
Regarding claim 1, the term “in proximity to” in the claim is a relative term which renders the claim indefinite. The term “in proximity to” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear how close, or far, the claimed variant nucleotide must be to a germline variant in order for one of ordinary skill in the art to perform linkage analysis or if there is no distance limit that a particular variant nucleotide can have to a germline variant. For example, is it enough that the variant nucleotide and germline variant be present on the same chromosome for them to be “in proximity” to one another? Or, must there be some pre-determined and pre-defined distance that the variant nucleotide and the germline variant must be from one another in order to consider them “in proximity” and perform the claimed linkage analysis?
Regarding claim 1, part (e), the claim recites the term “performing a linkage analysis” in lines 8-9 of the claim. The specification does not define what specific method steps are encompasses in the claimed “linkage analysis” and the claim does not recite any further method steps describing what one of ordinary skill in the art must do in order to successfully perform the claimed method step. Accordingly, it is unclear what method steps are encompassed by part (e) of the claim and how one of ordinary skill in the art would perform the claimed method.
Regarding claim 1, part (f), the claim recites that the identification of a variant nucleotide being present on the forward and reverse strands in the genomic DNA is determined “when the linkage analysis indicates that the variant nucleotide and the germline variant are linked” in lines 10-12 of the claim. Because the claimed “linkage analysis” is a method that does not have specific method steps, as described above, it is unclear what it means for the linkage analysis to determine that the claimed variant nucleotide and the germline variant are “linked”.
Regarding claims 4-7, as the claims are ultimately dependent on claim 1 and do not rectify the 35 USC 1129(b) rejection above, the claims are also rejected under 35 USC 112(b).
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 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 and 4-7 are is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bohrson (Bohrson, Craig L., et al. "Linked-read analysis identifies mutations in single-cell DNA-sequencing data." bioRxiv (30 October 2017)).
Regarding claim 1, Bohrson is directed towards a study concerned with linked-read analysis (i.e., LiRA) (Abstract). Bohrson teaches that LiRA is a method that utilizes phasing of somatic single nucleotide variants with nearby germline variants to identify true mutations, thereby allowing accurate estimation of somatic mutation rates at the single cell level (Abstract). Bohrson teaches that (a) single neurons are isolated and lysed such that genomic DNA can be analyzed (i.e., genomic DNA is purified), (b) the genomic DNA is amplified, and (c) the amplified genomic DNA is sequenced (see Figure 1a, Figure S1, and Figure Legends). Bohrson teaches that (d) candidate somatic-stranded single nucleotide variants (i.e., termed “false positives”) close to (i.e., interpreted as being “in proximity to”) germline variants can be identified (see Results; Figure 1). Bohrson teaches that (e) the SNV can be identified as being cis linked or trans linked to the germline variant (i.e., linkage analysis can be performed between the variant nucleotide and the germline variant) (see Figure 1 and Figure Legend). Bohrson teaches that (f) the variant nucleotide can be identified as a true somatic single nucleotide variant when the variant is present on both the forward and reverse strands and is trans linked to the germline variant (see Figure 1 and Figure Legend).
Regarding claim 4, Bohrson teaches that the cell is a neuron (see Figure 1, Figure S1, and Figure Legends).
Regarding claims 6-7, Bohrson teaches that DNA lesions induced during DNA amplification via polymerase errors that are present on only a single strand of the amplified genomic DNA can be identified and eliminated from sequence reads (see Figure 1b, Figure S1b, and Figure Legends).
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 factual inquiries 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.
Claim(s) 1 and 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dong (Nature methods 14.5 (2017): 491-493) in view of Usuyama "HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations." Bioinformatics 30.23 (2014): 3302-3309).
Regarding claim 1, the claimed somatic SNV that is “in proximity to” a germline variant such that they are indicated as being “linked” is interpreted as encompassing a variant nucleotide that is on the same chromosome of the germline variant. The claimed “linkage analysis” is interpreted as analysis that utilizes a comparison of a single cell’s sequenced genomic DNA to analyzed haplotypes of cell lines comprising a somatic SNV and a germline SNV derived from cell lines.
Dong is drawn to a study concerned with identification of single-nucleotide variants in whole-genome-amplified single cells (Abstract). Dong teaches the use of a method that comprises (a) purifying genomic DNA, (b) amplifying the purified genomic DNA, and (c) sequencing the amplified genomic DNA (pg. 494-495). Dong teaches that (d), (f) double-stranded SNVs can be detected by detecting variant nucleotides on forward and reverse strands of genomic DNA (pg. 495; see Supplementary Figure 1). Dong teaches the use of an algorithm that can detect true somatic SNVs of the single cell by comparing the detected SNVs to different alignment data in order to differentiate true somatic SNVs from PCR artifacts (pg. 492; see Supplementary Figure 7). Dong teaches that germline SNPs can be detected by the method and false positives of germline variants called, and compared to other cells’ germline variant calls, in order to determine if the germline variant is a true positive, a false negative, or a false positive (pg. 491-492; see Figures 1-2). Dong teaches that amplified single-cell data from cancer cells can be analyzed and the presence of the SNVs in the cancerous cells detected (pg. 492; see Figure 2; see “Public single-cell data”).
Dong does not teach or suggest that (d) the variant nucleotide is detected when the variant nucleotide is in proximity to a germline variant (Claim 1). Dong does not teach or suggest that (e) linkage analysis is performed between the variant nucleotide and the germline variant (Claim 1). Dong does not teach or suggest that (f) the variant nucleotide is identified when the linkage analysis indicates that the variant nucleotide and the germline variant are linked (Claim 1).
However, one of ordinary skill in the art would have considered the teachings of Usuyama as both references are common fields of endeavor pertaining to the detection of somatic SNVs via the analysis of sequenced genomic DNA.
Usuyama is directed towards a study concerned with the development of an algorithm, HapMuC, that can call somatic mutations near heterozygous germline variants (Abstract). Usuyama teaches that statistical approaches that allow distinction of true somatic mutations from relatively numerous germ line variants, sequencing errors, and alignment errors are required in order to detect somatic mutations that are associated with cancer (pg. 3302). Usuyama teaches that candidate somatic SNVs “near” (i.e., interpreted as being in proximity to and linked to) germline variants can be identified with the algorithm (i.e., linkage analysis may be performed on the somatic SNV and the germline SNV) and differentiated from the germline variant via haplotype analysis (pg. 3303; see Fig. 1). Usuyama teaches that genomic sequencing data from breast cancer cell lines (i.e., genomic data derived from cells) was able to be analyzed and the somatic SNVs near the germline SNVs identified and differentiated from the germline SNVs ( pg. 3306-3307; see Table 2). Usuyama teaches that the motivation for developing the algorithm derived from a need for accurate detection of somatic point mutations with low allele frequencies in impure and heterogeneous cancer samples (Abstract).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Dong such that linkage analysis was performed on the somatic and germline SNVs when the SNVs were in proximity to each other, such that the somatic SNV and the germline variant are identified as being linked, as described by Usuyama. A person of ordinary skill in the art would have been motivated to do so in order to accurately detect somatic point mutations that have a low allele frequency in the presence of relatively numerous germ line variants. A person of ordinary skill in the art would have had a reasonable expectation of success because both Dong and Usuyama teach the analysis of genomic data derived from cancerous cells that can identify the presence of somatic and germline SNVs in the amplified genomic sequences.
Regarding claim 4, Dong teaches that the single cell was a dermal fibroblast (i.e., a skin cell) (pg. 494).
Claim(s) 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dong (Nature methods 14.5 (2017): 491-493) in view of Usuyama "HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations." Bioinformatics 30.23 (2014): 3302-3309) as applied to claims 1 and 4 above, and further in view of Varma (Biotechnology Journal: Healthcare Nutrition Technology 2.3 (2007): 386-392).
Regarding claim 5, Dong in view of Usuyama renders obvious claims 1 and 4 as described above.
Dong in view of Usuyama does not teach or suggest that the purifying step comprises isolating the nucleus from the single cell (Claim 5).
However, one of ordinary skill in the art would have considered the teachings of Varma as both references are common fields of endeavor pertaining to the purification of DNA from target cells.
Varma is drawn to a stud concerned with plant genomic DNA isolation (Abstract). Varma teaches that it was known in the art that nuclei can be isolated from target cells before extraction of nuclear DNA (i.e., genomic DNA) in order to minimize contamination problems in the genomic DNA prior to amplification (pg. 389).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the genomic purification method step described by Dong in view of Usuyama for the purification step comprising isolating the nucleus from the cell, as described by Varma. A person of ordinary skill in the art would have been motivated to do so in order to utilize a DNA purification method step that was known to minimize contamination problems in isolated genomic DNA. A person of ordinary skill in the art would have had a reasonable expectation of success because both Dong in view of Usuyama and Varma teach the purification of genomic DNA from a target cell prior to amplification of the genomic DNA.
Claim(s) 6-7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dong (Nature methods 14.5 (2017): 491-493) in view of Usuyama ("HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations." Bioinformatics 30.23 (2014): 3302-3309) as applied to claims 1 and 4 above, and further in view of Kraytsberg (Methods 46.4 (2008): 269-273).
Regarding claims 6-7 Dong in view of Usuyama renders obvious claims 1 and 4 as described above.
Dong in view of Usuyama does not teach or suggest that the method comprises eliminating from a sequence read a variant nucleotide that is not present on forward and reverse strands, wherein the absence of the variant nucleotide on a forward or reverse strand identifies an error in genomic sequencing (Claim 6) derived from a DNA lesion that is generated during DNA amplification (Claim 7).
However, one of ordinary skill in the art would have considered the teachings of Kraytsberg as both references are common fields of endeavor pertaining to the study of the elimination of amplification errors in methods of identifying double-stranded mutations.
Kraytsberg is drawn to a study concerned with single molecule PRC in DNA mutational analysis (Abstract). Kraytsberg teaches that a genuine double stranded mutation in a double stranded DNA molecule can be differentiated from an DNA lesion derived from an amplification error by comparing the forward and reverse strands of the DNA molecule and determining if the variant nucleotide is absent on either the forward or reverse strand (pg. 270-271; see Fig. 1). Kraytsberg teaches that polymerase errors can be easily discriminated by direct sequencing of the PCR product (pg. 270).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method rendered obvious by Dong in view of Usuyama via the incorporation of a method step comprising comparing the forward and reverse strands of the DNA molecule and determining if the variant nucleotide is absent on either the forward or reverse strand in order to determine if the mutation is a genuine double-stranded mutation or a DNA lesion generated during amplification, as described by Kraytsberg. A person of ordinary skill in the art would have been motivated to do so in order to remove DNA lesions induced by polymerase errors derived from DNA amplification to correctly identify genuine double stranded mutations in target DNA. A person of ordinary skill in the art would have had a reasonable expectation of success because both Dong in view of Usuyama and Kraytsberg are drawn to studies concerned with detecting double-stranded mutation in DNA following the isolation and amplification of genomic DNA from a sample.
Response to Arguments
Applicant’s arguments with respect to claim(s) 1 and 4-7 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Insofar as Applicant’s arguments are applicable to the newly applied rejections of record, Applicant alleges that Dong does not anticipate the newly amended claims (Remarks; pg. 6-7). Applicant alleges that because Dong does not anticipate the newly amended claims, the previously filed 35 USC 103 rejections of claims 5-7 utilizing Varma and Kraytsberg do not render the newly amended claims obvious (Remarks; pg. 7-8).
This argument is not found persuasive because, as described above in the 35 USC 103 rejections of record necessitated by amendment, it is the combination of Dong and Usuyama that render the instantly claimed method obvious. Therefore, the previously utilized Varma and Kraytsberg references are interpreted as being drawn towards valid prior art in the 35 USC 103 rejections of claims 5 and 6-7.
Applicant alleges that a declaration under 37 CFR 1.130 has been filed which disqualifies the previously cited Lodato reference as a valid prior art reference.
This argument, and the declaration filed 10 December 2025, have been deemed persuasive. Accordingly, the previously pending 35 USC 102 rejection of claims 1 and 4-7 over the previously cited Lodato reference has been withdrawn.
Conclusion
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 KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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