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 .
DETAILED ACTION
1. The Applicant’s response to the office action filed on December 08, 2025 is acknowledged.
Status of the Application
2. Claims 1-18 are pending under examination. Claim 19 was canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive in-part for the following reasons.
Objection to the Specification-Maintained
3. The disclosure is objected to because of the following informalities:
(i) The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (at least page 130, line 1). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Response to Arguments:
With reference to the objection to the specification, the Applicant’s arguments and the amendment have been fully considered and found persuasive in-part. With reference to the embedded hyperlink or browser-executable code, the amendment did not address the browser-executable code (WWW) in table 4 and the objection is maintained.
4. The objection to the sequence identifiers has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 112-Withdrawn
5. The rejection of claims under 35 USC 112(b) has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 102-Withdrawn
6. The rejection of claim 1 under 35 USC 102(a)(1) as being anticipated by Agresti et al. has been withdrawn in view of the amendment.
7. The rejection of claims 1-9 and 13-19 under 35 USC 102(a)(1) as being anticipated by Kuchroo et al. has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 103-Withdrawn
8. With reference to the rejection of claims 1-19 under 35 USC 103 over Kuchroo et al. in view of Wen et al. has been withdrawn in view of the amendment.
New Rejections necessitated by the amendment
Claim Rejections - 35 USC § 112
9. 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 14 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. Claim 14 recites ‘a surface of a’. The limitations are unclear and indefinite because it is unclear whether the limitation is referring to a surface of a human body or is it referring to any surface of any body of an object.
Claim Rejections - 35 USC § 102
10. 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.
Claims 1-9 and 16-18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Abate et al. (US 2017/0009274).
Abate et al. teach a method of claim 1, for treating a cell population, the
method comprising (A) mixing an aqueous solution comprising a plurality of dispersed cell and an aqueous solution comprising solubilized cellular barcodes, each barcode having a different nucleotide sequence, thereby obtaining a droplet population from a cell dispersion comprising an isolated cell population, the droplet population comprising aqueous droplets, at least some of which each comprise one cell and one-molecule cellular barcode unique to one cell (para 0031-0033, 0007, 0016, 0141, 0163, 0279, 0120-0122 01458, Fig. 26, 2 and 7).
Abate et al. teach a method of claim 2, for analyzing nucleotide sequences of genes included in a cell population, the method comprising (A) mixing an aqueous solution comprising a plurality of dispersed cell and an aqueous solution comprising solubilized cellular barcodes, each barcode having a different nucleotide sequence thereby obtaining a droplet population from a cell dispersion comprising an isolated cell population, the droplet population comprising aqueous droplets, at least some of which each comprise one cell and one-molecule cellular barcode unique to the one cell (para 0031-0033, 0007, 0016, 0141, 0163, 0279, 0120-0122 01458, Fig. 26, 2 and 11); and
(B) obtaining an amplification product of the cellular barcode and an amplification product of a predetermined gene(antibody gene) in each obtained droplet, further obtaining a linked product comprising nucleotide sequences of the cellular barcode and all or some of the predetermined gene, and collecting the obtained linked product from the droplets into an aqueous solution and sequencing the obtained linked product to determine the nucleotide sequence of the predetermined gene and the nucleotide sequences of the cellular barcode (para 0031-0033, 0141, 0007, 0016, 0163, 0279, 0120-0122 1458, Fig. 26, 2 and 11).
With reference to claim 3, Abate et al. teach that wherein, in the (B), the amplification product of the cellular barcode has a first region derived from a first primer, the amplification product of the predetermined gene has a second region derived from a second primer, the first region and the second region have complementary sequence portions hybridizable with each other, the first primer and the second primer each have one or more tag molecules linked thereto, and the tag molecule is not included in the linked product; and the method further comprising removing the amplification product having a tag molecule from the linked products collected into the aqueous solution using a column or a bead carrying a molecule having an affinity for the tag molecule in the (B) (para 0016, 0125, 0141, 0138, 0229-0234, 0252, 0272-0273, 0292-0294).
With reference to claim 4-6, Abate et al. teach that the method further comprising (c )1) clustering the determined nucleotide sequences based on the determined nucleotide sequence of the cellular barcode to obtain a plurality of first clusters; further comprising (D-1) estimating the number of cells included in the cell population or the number of cells having a specific predetermined gene from the number of the obtained first clusters; and (C-2) clustering the determined nucleotide sequences based on the determined nucleotide sequence of the predetermined gene to obtain a plurality of second clusters (para 0026-0032, 0271, 0277-0280, 1346-01348).
With reference to claim 7, Abate et al. teach that the method further comprising (D-2) estimating the number of cell types included in the cell population from the number of the obtained second clusters (para 1462, 0026-0032, 0271, 0297).
With reference to claim 8, Abate et al. teach that the method further comprising (C-3) clustering the determined nucleotide sequences based on the determined nucleotide sequence of the cellular barcode to obtain a plurality of first clusters, and clustering the determined nucleotide sequences based on the determined nucleotide sequence of the predetermined gene to obtain a plurality of second clusters (para 0029-0032, 0271).
With reference to claim 9, Abate et al. teach that the method further comprising (D-3) determining the first cluster, into which the nucleotide sequence of the predetermined gene is classified, from the nucleotide sequence of a cellular barcode linked to the nucleotide sequence of the predetermined gene classified into at least one second cluster based on information on combinations of the obtained nucleotide sequence of the cellular barcode and the obtained nucleotide sequence of the predetermined gene, and estimating the number of cells classified into the second cluster from the number of the first clusters into which the cellular barcode is classified (para 0028-0034, 0194-0200, 0289, 0074-0077).
With reference to claim 16-18, Abate et al. teach that the first cell population and the second cell population are microbiotas obtained from different sites of same subject from different sites of the same subject at different time points (para 0130, 0204-0206, 0229, 0305). For all the above the claims are anticipated.
Claim Rejections - 35 USC § 103
11. 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.
Claims 1-18 are rejected under 35 U.S.C. 103 as being unpatentable over Abate et al. (US 2017/0009274) in view of Wright et al. (US 2019/0086410).
However, Abate et al. did not specifically teach classifying cluster data into cell-based taxonomic units and microbiota of the gastrointestinal tract of a subject.
Wright et al. teach a method for analyzing gut microbiota, wherein the method comprises analyzing amplification products by sequencing and processing sequence reads to classify the sequence data clusters and classifying the cluster into taxonomical units (OTUs) based on sequence similarities and abundance using 16S rRNA gene sequence reference, thereby classifying microbial communities in a sample (para 0223-0231).
It would have been prima facie obvious to an ordinary person skilled in the art before the effective filing date of the invention to modify the method of Abate et al. with classifying sequence similarity based operational taxonomical units as taught by Wright et al. to improve the method of analyzing microbiota. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would result in an improved microbiota sequence analysis because Wright et al. explicitly taught classification by sequencing of 16SrRNA gene and determining taxonomical units to differentiate various microbial communities of the gut (para 0228-0231) and such a modification is considered obvious over the cited prior art.
Conclusion
No claims are allowable.
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 SURYAPRABHA CHUNDURU whose telephone number is (571)272-0783. The examiner can normally be reached 8.00am-4.30pm.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681