Notice of Pre-AIA or AIA Status
Claims 226-245 are pending and examined herein.
Claims 1-225 are canceled.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claims 233, 240-241, and 244 are objected to because of the following informalities:
Claim 233 is missing a conjunction before “wherein” on line 3.
Claim 240 recites “the oligonucleotide molecules comprises the cleavage site”, which has improper subject-verb agreement.
Claim 241 recites two alternative methods using the indicators (i) and (2).
Claim 244 recites the phrase “said at least said subset of said plurality”.
Appropriate correction is required.
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.
Vickovic et al., Weinstein et al., and Zhou et al.
Claims 226-230, 235-236, 239-240, and 243-244 are rejected under 35 U.S.C. 103 as being unpatentable over Vickovic et al. (Nat. Meth. (2019), 16: 987-990; cited in IDS of 4/29/2025) in view of Weinstein et al. (Cell (2019), 178: 229-241; cited in IDS of 12/18/2023), as evidenced by Zhou et al. (Int. J. Biol. Sci. (2020), 16(14): 2663-2674).
Regarding claim 226, Vickovic discloses a method comprising:
providing a substrate comprising a plurality of beads immobilized to a plurality of individually addressable locations (p. 987, col. 1, ¶3), wherein said beads spatial tag molecules with spatial tags, and wherein each bead has a unique spatial tag (p. 987, col. 2, ¶1);
loading a sample onto the substrate, wherein the sample comprises a plurality of analyte sequences (p. 987, col. 1, ¶3);
releasing the spatial tag molecules from the beads (Methods, RNA-Seq library preparation and sequencing);
tagging a spatial tag to each of the analyte sequences to generate spatially tagged sequences (Fig. 1a, 2nd panel); and
generating a map of analyte sequences by identifying spatial tags, wherein the map comprises spatial information between the analyte sequences (Fig. 1a, 3rd panel).
Vickovic does not disclose that the location of the spatial tags are unknown prior to release, nor that the analyte sequences are tagged with at least two spatial tags.
Weinstein discloses a method of DNA microscopy where the location of the spatial tags is unknown prior to release (p. 230: “Here, we propose a distinct third modality for microscopy which requires neither optics nor physical capture from known coordinates”; Fig. 1A). Weinstein further discloses tagging analyte sequences with at least two spatial tags (Fig. 1D).
Zhou teaches that DNA barcode bead array methods – such as that of Vickovic – are limited by the “long and repeated imaging process” required to decode the positions of the spatial tags (Zhou, p. 2667, Barcoded bead array-based methods). Additionally, Weinstein discloses that DNA microscopy circumvents the need for array decoding by mapping analyte positions using relative proximities (Weinstein, p. 229, Summary). Therefore, there was motivation to apply the method of Weinstein to that of Vickovic in order to eliminate a lengthy and inefficient step.
As such, it would have been obvious to one of ordinary skill in the art by the effective filing date to apply the encoding strategy of DNA microscopy, as disclosed by Weinstein, to the bead array method of Vickovic. Furthermore, there would have been a reasonable expectation of success as many encoding methods were well-known (Zhou, Fig. 1), indicating that one of ordinary skill would have been able to draw from the large number of established techniques and knowledge in order to combine these methods.
Regarding claim 227, Vickovic further discloses loading the beads onto the substrate prior to (a) (Fig. 1a; Methods, Array generation).
Regarding claims 228-230, Vickovic further discloses that the sample is a tissue sample that is fixed (Methods, Tissue staining and imaging) and permeabilized (Methods, RNA-Seq library preparation and sequencing), and that the analyte sequences comprise a plurality of mRNA transcript sequences (“RNA-seq”).
Regarding claim 235 and 236, Vickovic further discloses that a bead comprises a set of spatial tag molecules, wherein each spatial tag molecule comprises a common spatial tag (Fig. 1a, 2nd panel) and a unique molecular identifier (Fig. 1a, 1st panel).
Regarding claims 239 and 240, Vickovic further discloses that a spatial tag molecule is an oligonucleotide molecule (p. 987, col. 1: “barcoded poly(d)T oligonucleotides”), and that the releasing comprises providing an enzyme mis comprising an enzyme configured to cleave or digest a cleavage site (Methods, RNA-Seq library preparation and sequencing), wherein the oligonucleotide molecule comprises the cleavage site (Fig. 1a, 1st panel).
Regarding claim 243, Vickovic further discloses that a plurality of beads comprises at least 1,000,000 beads (Methods, Array generation: “The complete bead pool was used to load a total of 1,467,270 individual hexagonal wells”).
Regarding claim 244, Vickovic further discloses that the spatial information comprises a relative position of analyte sequences with respect to a reference analyte sequence (Fig. 1a, 3rd panel).
Vickovic et al., Weinstein et al., Zhou et al., and Gunderson et al.
Claims 237 and 241 are rejected under 35 U.S.C. 103 as being unpatentable over Vickovic et al. in view of Weinstein et al., as evidenced by Zhou et al. and Gunderson et al. (Gen. Res. (2004), 14: 870-877).
Regarding claim 237, All limitations of claim 235 are considered obvious, as discussed above. Additionally, Vickovic discloses that the set of spatial tag molecules are linked to a bead using amine chemistry, as described in Gunderson (Methods, Bead production).
Gunderson discloses that, on average, each bead carries about 106 oligonucleotides (p. 875, Preparation of Oligonucleotide-Linked Beads and Bead Pools), indicating that a set of spatial tag molecules of Vickovic comprises at least 100,000 spatial tag molecules.
Regarding claim 241, Gunderson further discloses that a spatial tag molecule comprises a capture entity (p. 875: “oligonucleotides labeled at the 5’ terminus with a primary amine”) and Vickovic discloses that the method further comprises recovering a plurality of tagged complexes using the capture entity and generating spatially tagged sequences (Fig. 1a, 2nd and 3rd panels).
Vickovic et al., Weinstein et al., Zhou et al., and Fan et al.
Claims 231 and 238 are rejected under 35 U.S.C. 103 as being unpatentable over Vickovic et al., Weinstein et al., and Zhou et al. as applied to claims 226-230, 235-236, 239-240, and 243-244 above, and further in view of Fan et al. (US PGPub No: 2021/0095331).
Regarding claim 231, Vickovic further discloses generating a tagged complex (Fig. 1a, 2nd panel) and using the tagged complex to generate a spatially tagged sequence (Fig. 1a, 3rd panel), and Weinstein also discloses generating spatially tagged sequences (Fig. 1A-C). However, neither Vickovic nor Weinstein disclose a bridge construct that captures first and second spatial tag molecules and an analyte sequence.
Fan discloses a method for spatial transcriptomics that comprises contacting bridge constructs (p. 11, ¶[0094-5]: “ligation linkers”) with spatial tag molecules (p. 11, ¶[0094]: “barcoded polynucleotides”) under conditions sufficient for a bridge construct to capture (Fig. 5B) a first spatial tag molecule (“Barcode A”), a second spatial tag molecule (“Barcode B), and an analyte sequence (“mRNA”), to generate a tagged complex (Fig. 5B), and generating a spatially tagged sequence from the tagged complex (p. 13, ¶[0115]). Furthermore, Fan teaches that the concept of appending barcodes to nucleic acids is known in the art (p. 11, ¶[0096]).
Therefore, the methods of Vickovic, Weinstein, and Fan all generate spatially tagged sequences, using different methods of appending barcodes. As the methods of appending barcodes serve the same function in the described methods, it would have been obvious to one of ordinary skill in the art by the effective filing date to substitute the method of generating spatially tagged sequences of Fan for that of Vickovic and Weinstein. Furthermore, the results of such a substitution would have been predictable as the various methods of appending barcodes were well-understood by one of ordinary skill, as taught by Fan.
Regarding claim 238, Vickovic further discloses that the plurality of beads comprises a first set and a second set of beads wherein the first set of beads comprises a first set of spatial tag molecules and the second set of beads comprises a second set of spatial tag molecules (Fig. 1a, 2nd panel). However, Vickovic does not disclose that these spatial tag molecules each have two attachment sequences.
Fan discloses a first set of spatial tag molecules (Fig. 5B: “Barcode A”) that each comprise a first attachment sequence (“Poly-T”) and a second attachment sequence (“Ligation Linker”). Fan also discloses a second set of spatial tag molecules (Fig. 5B: “Barcode B”) that each comprise a third attachment sequence (“Ligation Linker”) and a fourth attachment sequence (“PCR handle”).
It would have been obvious to one of ordinary skill in the art to substitute the spatial tag method of Vickovic and Weinstein with that of Fan, based on the reasoning provided above. This substitution would predictably result in first and second sets of beads with first and second sets of spatial tag molecules, respectively, where the first and second sets of molecules comprise first and second or third and fourth attachment sequences, wherein the first attachment sequence is different from the third attachment sequence.
Vickovic et al., Weinstein et al., Zhou et al., and Ramachandran Iyer et al.
Claims 242 and 245 are rejected under 35 U.S.C. 103 as being unpatentable over Vickovic et al., Weinstein et al., and Zhou et al. as applied to claims 226-230, 235-236, 239-240, and 243-244 above, and further in view of Ramachandran Iyer et al. (WO 2020/176788).
Regarding claim 242, Vickovic further discloses that the spatial tag molecule comprises a cleavage site (Fig. 1a, 1st panel). However, Vickovic does not disclose that the spatial tag molecule comprises a blocking group.
Ramachandran Iyer discloses a method of spatial analysis where analytes are tagged with spatial barcodes. Additionally, Ramachandran Iyer discloses that spatial tag molecules comprise a blocking group (p. 247, line 3) and a cleavage site (p. 18, lines 25-27). Additionally, Ramachandran Iyer teaches that a blocking group of a spatial tag molecule can be used to selectively analyze certain regions of interest by blocking areas outside of that region (p. 246, lines 17-21; p. 247, lines 1-3). Therefore, it would have been obvious to one of ordinary skill in the art by the effective filing date to use a blocking group in the method of Vickovic, based on the motivation provided in Ramachandran Iyer to selectively analyze regions of interest. Additionally, one of ordinary skill in the art would have a reasonable expectation of success in doing so, as the blocking groups of Ramachandran Iyer (“blocking probes”) are used to block oligonucleotides immobilized on a substrate, like those of Vickovic.
Regarding claim 245, Vickovic does not disclose a second substrate. Ramachandran Iyer discloses, after loading a sample onto a first substrate and before generating spatially tagged sequences, contacting the sample with a second substrate (p. 386-7, line 20; lines 28-19). Ramachandran also teaches that contacting the sample with a second substrate allows for the analysis of analyte sequences from different regions of interest (p. 386, lines 25-27). Therefore, it would have been obvious to one of ordinary skill in the art by the effective filing date to similarly extend the method of Vickovic by the use of a second substrate, based on the motivation to investigate analyte sequences from multiple regions of interest. Furthermore, one of ordinary skill in the art would have a reasonable expectation of success because Vickovic and Ramachandran Iyer disclose methods for spatial transcriptomics using barcodes delivered to a sample by a substrate.
By extending the method of Vickovic to use a second substrate, the remaining limitations of claim 245 would be rendered obvious as they are disclosed by Vickovic regarding a single substrate. Additionally, it would be a matter of routine experimentation to include spatial tags that are mutually exclusive to those of the first plurality of spatial tags in order to facilitate downstream pooling and analysis, a concept which is well-known in the art.
Allowable Subject Matter
Claims 232-234 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Alexandra Olson whose telephone number is (571)272-7519. The examiner can normally be reached Monday-Friday 9-5pm.
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, Heather Calamita can be reached at (571) 272-2878. 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.
/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
Prosecution Insights