DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-5, 7, 9, 12, 23-25, 27-29 without traverse in the reply filed on 1/23/2026 is acknowledged. The claims 6, 8, 10, 11, 17, 18, 21, 22, 26, 30 and 31 have been canceled. The claims 13-16, 19 and 20 are withdrawn from consideration as being drawn to a non-elected invention.
Priority
This application claims benefit of 63/394,152 filed 08/01/2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/4/2024. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Drawings
The drawings were received on 12/4/2023 is acknowledged. These drawings are found acceptable by the examiner.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1 and 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mir et al (US 20210382056, December 2021, effective filing date 2015) in view of Choi et al (US 20200102614, April 2020).
Regarding claim 1, Mir teaches a method of quantifying an amount of mouse cells and human cells in a cell sample (Method for Rapid Accurate Dispensing, Visualization and Analysis of Single Cells, Title ... three samples were examined. Two samples were composed of a single species: human U87-MG-(Red Fluorescent protein positive) cells or mouse NIH/3T3 cells. The third sample was composed of a mixture of the individual single species samples, Para. [0112]; The bar graph indicates the relative cell counts from an on-chip dispense experiment, Para. [0032]), the method comprising: (a) assembling a single polymerase chain reaction (PCR) assay comprising template nucleic acid molecules from the cell sample and reagents suitable for the amplification of: (i) nucleic acid molecules comprising one mouse locus, (ii) nucleic acid molecules comprising a first human locus (That array was subsequently imaged, and single-cell containing wells selected and other analyte containing wells were selected to be processed into first and second strand cDNA. The cDNA was extracted from the chip using the methods described earlier. The cDNA was PCR amplified off-chip to yield DNA amplicon "libraries" suitable for NOS amplification and readout, Para. [0112]); (b) partitioning the PCR reaction assay into partitioned sections, wherein each partitioned section contains no target loci or a single locus, and wherein the locus can be amplified within the partitioned section (Such dispensing and cell detection may be repeated a number of times with respect to wells identified as having less than the pre-determined number of cells in order increase the number wells in the multi-well device containing the desired number (e.g., a single cell), Para. [0049]); (d) quantifying a number of partitioned sections having an amplification product corresponding to the mouse locus, an amplification product corresponding to the first human locus, and an amplification product corresponding to the second human locus (This method allows for quantification of mRNA transcripts in single cells and allows users to count the absolute number of transcript molecules/ cell to remove any variables from normalization, Para. [0104]); and (e) determining a Poisson-modeled number of partitioned sections having an amplification product corresponding to the mouse locus, a Poisson-modeled number of partitioned sections having an amplification product corresponding to the first human locus, and a Poisson-modeled number of partitioned sections having an amplification product corresponding to the second human locus, thereby determining an amount of mouse cells and human cells in the cell sample (method that employs Poisson statistics, Para. [0055]; Sequence reads from the sample libraries can then be mapped to the specific sample (i.e., species genome) to confirm firstly that the cell and RT buffer selection process were capable of selecting specific wells, and secondly, that selected wells from the mixed cell sample give rise to sequencing reads mapping to only one species. In effect, the latter can be used to calculate the single cell occupancy and partitioning ability of the system, Para. [0112]).
Mir fails to explicitly disclose (iii) nucleic acid molecules comprising a second human locus; a single PCR reaction assay; and (c) performing the single polymerase chain reaction assay.
Choi et al teaches nucleic acid molecules comprising a second human locus (Oligonucleotide primers for amplifying a human albumin gene, a mouse albumin gene, a human Papola gene, and a mouse Papola gene were designed, appropriate real-time PCR conditions ere established, (para. [0020]); a single PCR reaction assay and performing the single polymerase chain reaction (method for determining cross contamination of mouse genes for human cells in a patient-derived xenograft cell(s) [0020].
It would have been prima facie obvious to one of ordinary skill in the art at the time of the claimed invention to have been motivated to modify the quantification method Mir with the quantification method of Choi et al. The ordinary artisan would have been motivated to do so for the obvious benefit of detecting human genes in a cell mixture comprising both human and mouse cells.
Regarding Claim 23, Mir discloses a method of quantifying an amount of mouse cells and human cells in a cell sample (Method for Rapid Accurate Dispensing, Visualization and Analysis of Single Cells, Title; In this example, three samples were examined. Two samples were composed of a single species: human U87-MG-(Red Fluorescent protein positive) cells or mouse NIH/3T3 cells. The third sample was composed of a mixture of the individual single species samples, Para. [0112]), the method comprising: (a) assembling a single polymerase chain reaction (PCR) assay comprising template nucleic acid molecules from the cell sample and reagents suitable for the amplification of: (i) nucleic acid molecules comprising one mouse locus and (ii) nucleic acid molecules comprising a first human locus (That array was subsequently imaged, and single-cell containing wells selected and other analyte containing wells were selected to be processed into first and second strand cDNA. The cDNA was extracted from the chip using the methods described earlier. The cDNA was PCR amplified off-chip to yield DNA amplicon "libraries" suitable for NGS amplification and readout, Para. [0112]); (b) partitioning the single PCR reaction assay into partitioned sections, wherein each partitioned section contains no target loci or a single locus, and wherein the locus can be amplified within the partitioned section (Such dispensing and cell detection may be repeated a number of times with respect to wells identified as having less than the pre-determined number of cells in order increase the number wells in the multi-well device containing the desired number (e.g., a single cell), Para. [0049]); (d) quantifying a number of partitioned sections having an amplification product corresponding to the mouse locus and an amplification product corresponding to the first human locus (This method allows for quantification of mRNA transcripts in single cells and allows users to count the absolute number of transcript molecules/cell to remove any variables from normalization, Para. [0104]); and (e) determining a Poisson-modeled number of partitioned sections having an amplification product corresponding to the mouse locus and a Poisson-modeled number of partitioned sections having an amplification product corresponding to the first human locus, thereby determining an amount of mouse cells and human cells in the cell sample (The present disclosure provides, in certain embodiments, a simple, robust commercially applicable method that employs Poisson statistics, Para. [0055]; Sequence reads from the sample libraries can then be mapped to the specific sample (i.e., species genome) to confirm firstly that the cell and RT buffer selection process were capable of selecting specific wells, and secondly, that selected wells from the mixed cell sample give rise to sequencing reads mapping to only one species. In effect, the latter can be used to calculate the single cell occupancy and partitioning ability of the system, Para. [0112]).
Mir et al fail to explicitly disclose (c) performing the single polymerase chain reaction assay.
Choi teaches nucleic acid molecules comprising a second human locus (Oligonucleotide primers for amplifying a human albumin gene, a mouse albumin gene, a human Papola gene, and a mouse Papola gene were designed, appropriate real-time PCR conditions were established, Para. [0020]); a single PCR reaction assay and performing the single polymerase chain reaction assay (Method for determining cross contamination of mouse genes for human cells in a patient-derived xenograft cells, Title; the real-time PCR was performed by a single PCR, Para. [0020]).
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 Mir by performing a single PCR assay on a plurality of human genes as taught by Choi for the obvious benefit of increasing efficiency of detecting and identifying human genes in a cell mixture of mouse and human cells.
10. Claims 2 and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mir et al (US 20210382056, December 2021, effective filing date 2015) in view of Choi et al (US 20200102614, April 2020) as previously discussed above and further in view of Ginis et al. (hereinafter, "Ginis") (Developmental Biology, vol. 269, pages 360-380, 2004, citation made of record on IDS filed 4/4/2024).
Regarding claim 2 and 12, Mir in view of Choi teaches of quantifying mouse and human cells in a mixed sample as previously described above.
The references fail to explicitly disclose wherein if there is a discrepancy of at least about 10% between the Poisson-modeled number of partitioned sections having an amplification product corresponding to the first human locus and the Poisson-modeled number of partitioned sections having an amplification product corresponding to the second human locus, and then (e) assembling a single polymerase chain reaction (PCR) assay comprising template nucleic acid molecules from the sample and reagents suitable for the amplification of nucleic acid molecules comprising one mouse locus and a third human locus, (f) partitioning the single PCR reaction assay into partitioned sections, wherein each partitioned section contains no target loci or most often a single locus, and wherein the locus can be amplified within the partitioned sections; (g) performing the single polymerase chain reaction assay; (h) quantifying a number of partitioned sections having an amplification product corresponding to the one mouse locus and the third human locus; and (i) determining a Poisson-modeled number of partitioned sections having an amplification product corresponding to the one mouse locus and the third human locus, and averaging the number of partitioned sections from two out of the first human locus, the second human locus, and the third human locus in closest agreement.
Choi teaches nucleic acid molecules comprising a second human locus (Oligonucleotide primers for amplifying a human albumin gene, a mouse albumin gene, a human Papola gene, and a mouse Papola gene were designed, appropriate real-time PCR conditions were established, Para. [0020]); a single PCR reaction assay and performing the single polymerase chain reaction assay (Method for determining cross contamination of mouse genes for human cells in a patient-derived xenograft cells, Title; the real-time PCR was performed by a single PCR, Para. [0020]).
In a similar endeavor to Choi, Ginis teaches three or more human loci (Differences between human and mouse embryonic stem cells, Title; Table 1 lists the primers used for RT-PCR, Pg. 364, left column, first full paragraph; Table 1 discloses loci unique to mice and humans for detecting mouse and/or human cells).
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 Mir in view of Choi et al by using three or more human loci as taught by Ginis. The ordinary artisan would have been motivated to do so for the obvious benefit maximizing the accuracy of detecting human cells in a mixture of cells.
11. Claims 3 and 24 lack an inventive step under PCT Article 33(3) as being obvious over Mir et al (US 2021/0382056) in view of Choi (US 2020/0102614) as previously discussed above and further in view of Zhang (US 2020/0032332).
Regarding claims 3 and 24, Mir in view of Choi teach the method claim 1 as previously described above.
Mir in view of Choi fail to explicitly disclose wherein at least one of the human loci is stable in cancer.
Zhang teaches human loci stable in cancer (a second-generation sequencing-based method for simultaneously detecting microsatellite locus stability (Abstract; Detection maps of nine marker loci of a MSS cancerous tissue (corresponding to RS1608839FFP in Table 7) and its paired para-cancerous tissues in PCR detection, Para. [0039] – [0042] and [0047]).
It would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have of Mir and Choi to encompass human loci stable in cancer as taught by Zhang. The ordinary artisan would have been motivated to do so for the obvious benefit of ensuring accurate results from a single PCR assay in both cancer and normal cells.
12. Claims 4 and 25 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mir et al (US 20210382056, December 2021, effective filing date 2015) in view of Choi et al (US 20200102614, April 2020) as previously discussed above and further in view of Aujean et al (Biotechniques, 68(4), 219-222, 2020) and Reese et al (US 2017/0089903), (citation made of record on IDS 4/4/2024).
Regarding claims 4 and 25, Mir in view of Choi discloses the method of claim 1 as previously discussed above.
The references fail to explicitly disclose wherein the mouse locus is from a beta-2 microglobulin (B2m) gene and wherein the first human locus and the second human locus is from a serine/arginine-rich splicing factor (SRFS4) gene, an importin 8 (IP08) gene, or a splicing factor 3a protein complex (SF3A 1) gene.
Aujean teaches detection of mouse beta-2 microglobulin (Mouse ... B2m gene primers (Table 1) allowed the amplification of PCR products of 350 and 120 bp, respectively, from DNA (100 ng) extracted from mouse mammary gland whole mounts by standard PCR (45 cycles) (Figure 1C), Pg. 220, left column, first paragraph).
Reese teaches detection of SF3Al (detection of ... one or more SF3Al, Para. [0071]; Gene expression levels also can be determined by quantification of a microRNA or gene transcript (e.g., mRNA). Commonly used methods known in the art for the quantification of rnRNA expression in a sample include ... PCR-based methods, such as reverse transcription polymerase chain reaction (RT-PCR) and real time quantitative PCR (also referred to as qRT-PCR), Para. [0086]).
It would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to modify the method of Mir in view Choi to encompass detecting B2m and SF3A1 as taught by Aujean and Reese. The ordinary artisan would have been motivated to do so for the benefit of detecting the presence of a gene specific to mouse cells and human cells for the detection of human cells in a mixed cell sample.
13. Claims 2 and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mir et al (US 20210382056, December 2021, effective filing date 2015) in view of Choi et al (US 20200102614, April 2020) and Ginis et al. (hereinafter, "Ginis") (Developmental Biology, vol. 269, pages 360-380, 2004, citation made of record on IDS filed 4/4/2024) and previously discussed above and further in view of Aujean et al (Biotechniques, 68(4), 219-222, 2020) and Reese et al (US 2017/0089903), (citation made of record on IDS 4/4/2024).
Regarding Claim 5, Mir in view of Choi and further in view of Ginis discloses the method of claim 2.
The references fail to explicitly disclose wherein the mouse locus is from a B2m gene and wherein the first human locus, the second human locus, and the third human locus are from a SRFS4 gene, an IP08 gene, or a SF3Al gene.
Aujean teaches detection of mouse beta-2 microglobulin (Mouse ... B2m gene primers (Table l) allowed the amplification of PCR products of 350 and 120 bp, respectively, from DNA (l00 ng) extracted from mouse mammary gland whole mounts by standard PCR (45 cycles) (Figure lC), Pg. 220, left column, first paragraph).
Reese teaches detection of SF3A1 (detection of ... one or more SF3A1, Para. [0071]; Gene expression levels also can be determined by quantification of a microRNA or gene transcript (e.g., mRNA). Commonly used methods known in the art for the quantification of rnRNA expression in a sample include ... PCR-based methods, such as reverse transcription polymerase chain reaction (RT-PCR) and real time quantitative PCR (also referred to as qRT-PCR), Para. [0086]).
It would have been obvious to one of ordinary skill in the art in the art at the time of the effective filing date of the claimed invention to encompass detecting mouse beta-2 microglobulin as taught by Aujean and SF3A1 as taught by Reese in the method of Mir, Choi and Ginis. The ordinary artisan would have been motivated to do for the benefit of detecting a mouse cells and/or human cells in a mixed cell sample
14. Claims 7, 27 and 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mir et al (US 20210382056, December 2021, effective filing date 2015) in view of Choi et al (US 20200102614, April 2020) and further in view of Schumm et al (US 5,843,660).
Regarding Claim 7, 27 and 28, Mir in view of Choi disclose the method of claim 1 as previously discussed above.
The references fail to explicitly disclose wherein the method further comprises amplifying and detecting two or more human short tandem repeats (STRs) of microsatellite regions.
Schumm teaches amplifying and detecting two or more human short tandem repeats (STRs) of microsatellite regions such as D5S818 and D7S820 (A method of simultaneously determining the alleles present in at least four short tandem repeat loci from one or more DNA samples, comprising: (a) obtaining at least one DNA sample to be analyzed, (b) selecting a set of at least four short tandem repeat loci of the DNA sample to be analyzed which can be amplified together, wherein the at least four loci in the set are selected from the group of loci consisting of ... D5S8 l 8, D7S820 ... (c) co-amplifying the loci in the set in a multiplex amplification reaction, wherein the product of the reaction is a mixture of amplified alleles from each of the co-amplified loci in the set; and (d) evaluating the amplified alleles in the mixture to determine the alleles present at each of the loci analyzed in the set within the DNA sample, Claim 1).
It would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have modified the Mir in view of Choi by detecting STRs as taught by Schumm. The ordinary skill in the art would have been motivated to do so for the benefit of maximizing the accuracy of detecting mouse and/or human cells in a mixed cell sample.
15. Claims 9 and 29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mir et al (US 20210382056, December 2021, effective filing date 2015) in view of Choi et al (US 20200102614, April 2020) and further in view of Price et al (US 6,277,582).
Regarding claims 9 and 29, Mir et al in view of Choi discloses the method of claim 1 as previously discussed above.
The references fail to explicitly disclose wherein one or more Mycoplasma nucleic acid molecules are also amplified.
Price teaches one or more Mycoplasma nucleic acid molecules are amplified (Amplification primers and methods for specific amplification and detection of a Pl target are disclosed. The primer-target binding sequences are useful for amplification and detection of Mycoplasma pneumoniae target in a variety of amplification and detection reactions, Abstract; A method for detecting the presence or absence of Mycoplasma pneumoniae organisms in a sample, said method comprising: a) treating said sample using a pair of nucleic acid primers in a nucleic acid amplification reaction wherein a first primer consists of MP1Lprim (SEQ ID NO: 1) and a second primer consists of MP1Rprim1 (SEQ ID NO: 2), and b) detecting any amplified nucleic acid product, wherein detection of amplified product indicates presence of Mycoplasma pneumoniae organisms, Claim 17).
It would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to modify the method of Mir and Choi to encompass steps of amplifying Mycoplasma nucleic acid molecules as taught by Price. The ordinary artisan would have been motivated to so for the benefit of determining the presence or absence of Mycoplasma to determine if a mixed cell sample has been contaminated.
Conclusion
16. No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681
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