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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 9/5/2025 has been entered.
The claims filed 9/5/2025 are under consideration.
The amendments and arguments presented in the papers filed 9/5/2025 ("Remarks”) have been thoroughly considered. The issues raised in the final Office action dated 5/5/2025 listed below have been reconsidered as indicated.
a) The rejections of claim(s) 1-3, 7-9, 11-12, 18-21 and 24-25 under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Hill (WO 2016/077750) are withdrawn in view of the amendments to the claims.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New grounds of rejection necessitated by amendment are detailed below.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 9, 11-14, 17-22 and 24-29 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
The following are new rejections modified by the amendments to the claims.
The claim(s) recite(s):
“determining a copy number of the at least one target cell and/or cell-free nuclei or set of targets for individual partitions using the amplification data” (claim 1);
“enumerating cells and/or cell-free nuclei having an abnormal and a normal copy number of the target or set of targets” (claim 1);
“identifying partitions that contained no intact cells or nucleus when formed, based on the amplification data” (claim 17);
“comparing the copy number to at least one threshold” (claim 22);
“diagnosing aneuploidy or cancer if comparing meets one or more predefined criteria” (claim 22);
“identifying partitions that contained two or more cells and/or cell-free nuclei when formed, based on the amplification data” (claim 28); and
“excluding from the amplification data used in the determining step the detected photoluminescence from the identified partitions” (claim 28).
The number of partitions is not limited and broadly encompasses two partitions. The two partitions may contain only a single cell and only a single target is amplified. Thus, the amount of data that must be collected and/or analyzed by the claimed methods is minimal and may be managed by the human mind.
Each of the beforementioned embodiments are data processing steps that may be performed in a purely mental manner or with the aid of pen and paper.
The “determining” of a copy number step broadly encompasses mentally considering the amplification data from two partitions involving a single target in a single cell in order to reach a decision. This amounts to a very limited amount of data that is to be considered.
The “enumerating” of cells broadly encompassing simply counting the number of the partitions with a particular feature.
The “identifying” of partitions step broadly encompasses the consideration of amplification data from two partitions and reaching a decision regarding the partitions.
The “comparing” of the copy number step broadly encompasses comparing two copy number values to a threshold, which given the small amount of data as described above may be carried out in the mind.
The “diagnosing” of aneuploidy or cancer step broadly encompasses making a decision based on a limited amount of data.
The judicial exceptions are not integrated into a practical application because the claims do not involve: improvements to the functioning of a computer or to any other technology or technical field; applying or using the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition; applying the judicial exception with, or by use of, a particular machine; or effecting a transformation or reduction of a particular article to a different state or thing. The claimed limitations add insignificant extra-solution activity to the judicial exceptions. See MPEP 2106.05(g).
The claim(s) does/do not include additional elements, in particular the steps of “forming partitions”, “lysing cells and/or cell-free nuclei”, “selectively cleaving a DNA of the cells and/or cell-free nuclei “ and “performing at least one amplification reaction”, that are sufficient to amount to significantly more than the judicial exception because the claims encompass the use commercially available apparatus and methods as described in the instant specification (p. 4-5).
The claims also encompass the methods described Hill (WO 2016/077750 A1; previously cited) and/or Bailey (WO 2015/134523 A1).
Response to the traversal of the 101 rejections
The Remarks summarize the analysis for patentable subject matter eligibility under 35 USC 101 (p. 7).
The Examiner’s position is consistent with the guidance set forth in the MPEP.
The Remarks argue claim 1 has been amended to recite 'selectively cleaving a DNA of the cells and/or cell-free nuclei in the partition with a heat sensitive reagent, after lysing'. The Remarks argue the added limitation is not insignificant extra-solution activity, and that therefore the claim recites significantly more than the judicial exceptions identified by the Examiner. See p. 7.
The arguments have been fully considered but are not persuasive. The Remarks do not explain why the added limitation is not insignificant extra-solution activity. The amended element relates to data gathering and does not integrate the above identified judicial exceptions.
The Remarks argue Hill fails to teach or suggest cleaving DNA; and, therefore the limitation is not well-known under MPEP 2106.05(g) (1). See p. 8.
The arguments have been fully considered but are not persuasive. The claims encompass the use commercially available apparatus and methods as described in the instant specification. The Remarks do not address this description by the instant specification acknowledging that readily available products and methods may be used in the method. Furthermore, Hill and Bailey demonstrates that these processes were known at the time of filing.
The Remarks argue the linearization of a template by DNA cleavage provides efficient access to target sequences, thereby producing "more tightly clustered amplification signals for each type of partition, and thus more accurate assignment of partition types and determination of copy numbers" and therefore the limitation imposes meaningful limits on the claim such that it is not nominally or tangentially related to the invention, and is significant under MPEP 2106.05(g) (2). See p. 8.
The arguments have been fully considered but are not persuasive. While the elements of the claims are limiting, they relate to data gathering and involve routine and conventional techniques known in the field. As such, the limitations do not integrate the judicial exceptions identified or add significantly more to the judicial exceptions.
The Remarks argue the cleavage of DNA is part of the physical preparation of the sample, and is not part of either gathering or outputting data and therefore the limitation is not necessary data gathering and outputting under MPEP 2106.05(g). See p. 8.
The arguments have been fully considered but are not persuasive. The cleavage of DNA does not integrate the judicial exceptions. The manner of DNA cleavage is not limited by or informed by the judicial exceptions. The DNA cleavage does not add significantly more to the judicial exceptions because it was known as demonstrated by the specification and by Hill and/or Bailey. The DNA cleavage relates to data gathering as sample preparation is all under the umbrella of data gathering. If the sample is not prepared, no data can be gathered.
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.
Claim 9 is 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.
The following are new rejections necessitated by the amendments to the claims.
Regarding claim 9, the claim is incomplete because it depends from now cancelled claim 8.
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) 1-3, 9, 11, 12, 18, 19, 20 21, 25, 26 and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hill (WO 2016/077750 A1; previously cited) in view of Bailey (WO 2015/134523 A1).
The claim states “each target of the set of targets represents the same chromosome in the cells and/or cell-free nuclei”. The claim broadly encompasses also copy numbers based on “at least one target”, which is not limited to be representing the same chromosome.
Regarding claims 1 and 25, Hill teaches forming partitions that include a portion of a diluted sperm sample by pipetting 1 ul of a specimen at concentration of 0.8 cells/ul or 0.4 cells/ul into the wells of a 96 well PCR plate (para. 109-110). This results in forming 1 ul partitions of the diluted sperm sample. Because the concentration of the cells is less than 1 per ul, a subset of the partitions only contains one of the sperm cells and others contain none. Hill teaches the specimens included two populations of cells, a first population null for the target and a second population positive for the target (para. 124), such as CFTR or SMN. The target being at least one target as broadly encompassed by the claim.
Hill teaches lysing the cells from the sample in the partitions using 5 ul of lysis buffer in the well (para. 110). Hill teaches the use of proteinase K in the lysis buffer (para. 8, 80, 81 and 110).
After the cells are lysed, the proteinase K continues to selectively cleave intracellular proteins of the cells that have been released from the cell.
It is noted the claim does not limit the conditions for lysing the cells and/or cell-free nuclei from the sample in the partitions. For example, the claims do not specify that a heat sensitive reagent which selectively cleaves DNA of the cells is absent during the “lysing” step. The claim does not limit when or how a “heat sensitive reagent” is added or deployed for “cleaving a DNA of the cells and/or cell-free nuclei”.
Hill does not specifically teach selectively cleaving DNA of the cells and/or cell-free nuclei in the partition with a heat sensitive reagent after lysing.
However, Baily teaches formation of droplets containing cells which are lysed and the released DNA is selectively cleaved with MNase (Fig. 1A, 1B). MNase is a heat sensitive reagent which is able to be inactivated heating to at least 65o C for at least 10 minutes. The cleaved DNA is then subjected to a PCR reaction, for example using a QX-100 PCR system (Fig. 1A, 1B).
It would have been prima facie obvious to the ordinary artisan at the time of filing to have modified the method of Hill by incorporating the MNase treatment of Bailey. One would have been motivated to make such a change as it cleaves genomic DNA into mono-, di- and tri-nucleosome sized fragments (p. 2, 4 and 5) and it cleaves DNA without destroying epigenetic information (p. 31).
Hill teaches genomic DNA as a linearized template for amplification (para. 86, 89), in the form of a nucleic acid strand template. See also, Fig. 1.
Hill teaches performing an amplification reaction for a target within the partition wells (para. 110-111). Hill teaches the PCR reaction has a predefined number of 60 cycles (para. 110).
Hill teaches collecting amplification data from a quantitative PCR method carried out in each partition (para. 100, 101, 110 and 123; and Fig. 2). Hill teaches collecting photoluminescence by collecting fluorescence (para. 7, 63 and 98). The quantitative PCR method data as depicted in Fig. 2 is collected in an exponential and/or linear phase of the PCR reaction. The amount of photoluminescence from the fluorescent moieties corresponds to the amount of the target in the partition.
Hill teaches determining a copy number of the amplified target (para. 123-125). Hill further teaches duplications or deletions of targets, e.g., CFTR or SMN, are analyzed.
Hill teaches determining the ratio of SMN to the reference gene CFTR (para. 124).
Hills teaches enumerating the cells that have an abnormal copy number, i.e., null for the target, and a normal copy number, i.e., the target is present (para. 124).
Regarding claim 2, Hill teaches as depicted in Fig. 2, all the data collected for the cycles was used to determine the copy number of the target.
Regarding claim 3, Hill further teaches enumerating the partitions having the first or second populations (para. 124).
Regarding claim 9, Hill teaches some partitions have cells null for the target SMN and others have the SMN target as noted above, meaning the intensity of the signal varies between the partitions based on the number of targets present.
Regarding claim 11, Hill teaches amplifying two targets, CFTR and SMN, as described above. The copy number of each is determined based on the quantitative PCR method. See para. 109-127.
Regarding claim 12, Hill teaches amplifying two targets, CFTR and SMN, as described above. The two targets represent two different chromosomes as CFTR is on chromosome 7 and SMN is on chromosome 5.
Regarding claim 18, Hill teaches emulsion droplets in which aqueous droplets are surrounded by an immiscible liquid (para. 37 and 65).
Regarding claim 19, Hill teaches each partition is from the same diluted sperm sample, and a second fluid having PCR reagents is added after lysis (para. 109-110).
Regarding claim 20, Hill teaches adding 1 ul of a 0.8 cells/ul or 0.4 cells/ul solution to the partition wells as described above. On average each 1 ul partition has less than 1 cell per partition.
Regarding claim 21, Hill teaches collecting amplification reporting signals from the partitions and clustering partitions that are null or positive for the target as have the same copy number to each respective partition of the null or positive group. See paras. 110-124. Finding a “null” group is determining a deletion of the set of targets using the amplification data.
Regarding claim 24, Hill teaches adding the proteinase K to the partitions or “reaction vessels” as the heat sensitive reagent as described above.
Bailey teaches adding MNase after lysis as described above as a heat sensitive reagent.
Regarding claim 26, Hill teaches pipetting 1 ul of a specimen at concentration of 0.8 cells/ul or 0.4 cells/ul into the wells of a 96 well PCR plate (para. 109-110). Using a concentration of 0.4 cells/ul results in around 40% of the wells having a single cell.
Regarding claim 27, Hill does not teach the number of partitions having at least one cell or cell-free nucleus from the sample.
However, Bailey teaches that controlling size and formation of droplets were known. Bailey further teaches that the cell encapsulation rate can be optimized to achieve an average density of about 1 cell/droplet, or less, such as less than about 0.95 cells/droplet, less than about 0.9 cells/droplet, less than about 0.8 cells/droplet, less than about 0.7 cells/droplet, less than about 0.6 cells/droplet, less than about 0.5 cells/droplet, less than about 0.4 cells/droplet, less than about 0.3 cells/droplet, or less than about 0.2 cells/droplet, such as 0.1 to 1 cell/droplet. Bailey further teaches this results in the cells being contained such that no more than about 10%, no more than about 5%, no more than about 3%, no more than about 1%, or no more than 0.1% of the droplets contains more than one cell. See p. 50.
It would have been prima facie obvious to have modified the method of Hill to optimize the number of partitions having a cell within them based on the guidance of Bailey. Bailey demonstrates such an encapsulation rate can be controlled based on the desire of the user.
Claim(s) 13, 14, 17 and 22 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hill (WO 2016/077750 A1; previously cited) in view of Bailey (WO 2015/134523 A1) as applied to claims, 1, 11, 12 above and in further view of Oliphant (WO 2010/075459 A1; previously cited).
The following are new rejections necessitated by the amendments to the claims.
The claim states “each target of the set of targets represents the same chromosome in the cells and/or cell-free nuclei”. The claim broadly encompasses also copy numbers based on “at least one target”, which is not limited to be representing the same chromosome.
Regarding claims 13, 14, 17 and 22, Hill teaches the element of claims 1, 11 and 12 as required by claims 13, 14, 17 and 22 as described above.
Regarding claim 13, Hill further teaches amplifying two targets, CFTR and SMN, as described above. The copy number of each is determined based on the quantitative PCR method. See para. 109-127.
Hill teaches amplifying two targets, CFTR and SMN, as described above. The two targets represent two different chromosomes as CFTR is on chromosome 7 and SMN is on chromosome 5.
Hill does not specifically teach the elements of claims 4, 5, 13, 14, 17 and 22.
However, Oliphant teaches methods for determining the copy of targets based on nucleic acid amplification, that is analogous to that of Hill.
Regarding claims 4-5 and 14, Oliphant teaches the sample is a mix of fetal and maternal cells (para. 100) and in the case of fetal aneuploidy, the two populations have different copy numbers for a chromosome (para. 103). The maternal cells have 2 copies of the target and the fetal cells have 3 copies of the target (para. 103).
Regarding claim 13, Oliphant teaches the analysis and copy number determination of chromosomes 1 and 21 by genotyping SNPs on both chromosomes using a Taqman® assay (para. 80, 91). Chromosome 1 is less susceptible to aneuploidy because the aneuploidy is incompatible with viability (para. 80).
Regarding claim 17, Oliphant teaches enumerating the partitions with one of the two populations, 50,000 partitions with no heterogenous genotypes based on SNPs in chromosome 1 and 21 with no abnormal copy number and no target fetal cells, 50,000 partitions with some heterogeneous on chromosome 1 and a homozygous SNP on chromosome 21, and 50,000 partitions with some heterogenous genotypes on chromosome 21 with an abnormal copy number (para. 102-103).
Regarding claim 22, Oliphant teaches comparing the copy number to a threshold to diagnose an aneuploidy as trisomy 21 (para. 103). See also para. 66.
It would have been prima facie obvious to the ordinary artisan at the time of filing to have modified the method of Hill by substituting for the cellular sample, nucleic acid targets and copy number analyses of Oliphant. One would have been motivated to make the substitution as it permits one to detect copy number variations within fetal cells. The modification has a reasonable expectation of success as by Hill and Oliphant focus on methods relying a single cell analysis for copy number variations, that including partitioning cells and PCR amplification.
Claim(s) 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hill (WO 2016/077750 A1; previously cited) in view of Bailey (WO 2015/134523 A1) as applied to claims 1 above and in further view of Ness (US 2012/0194805 A1; previously cited).
Regarding claim 28, the combination of Hill and Bailey renders obvious the elements of claim 1 as encompassed by claim 28.
The combination does not specifically teach identifying partitions that contain two or more cells or cell-free nuclei based on amplification data and excluding the amplification data from those partitions form being used in the determining step.
Hill teaches separating out droplets/partitions that have more than one cell (para. 67).
Ness teaches detecting signals and determining whether an droplet should be excluded from analysis (para. 61).
It would have been prima facie obvious in view of the art as whole that based on amplification data, droplets with more than one cell can be identified and excluded from the analysis because it does not contain a single cell.
Claim(s) 29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hill (WO 2016/077750 A1; previously cited) in view of Bailey (WO 2015/134523 A1) as applied to claims, 1, 11, 12 above and in further view of Schoendube (Biomicrofluidics. 2015. 9:014117, 9 pages).
Regarding claim 29, the combination of Hill and Bailey renders obvious the elements of claim 1 as encompassed by claim 29.
The combination does not specifically teach forming partitions includes triggering droplet formation when and only when a cell or nucleus is present.
However, Schoendube teaches such elements were known.
Schoendube teaches isolating single cells form a sample by displacing the cell when detected by electrodes into a single-cell droplet that is then placed in a micro well plate.
It would have been prima facie obvious to the ordinary artisan to have modified the combined method of Hill and Bailey by replacing the single-cell droplet method with the technique of Schoendube. One would have been motivated to use the technique of Schoendube because it uses a more compact system relative to optical cell detection and smaller droplet size (p. 2).
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682