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Patent Application 18989119 - Compositions and Methods for Analyte Detection - Rejection

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Patent Application 18989119 - Compositions and Methods for Analyte Detection

Title: Compositions and Methods for Analyte Detection

Application Information

  • Invention Title: Compositions and Methods for Analyte Detection
  • Application Number: 18989119
  • Submission Date: 2025-05-23T00:00:00.000Z
  • Effective Filing Date: 2024-12-20T00:00:00.000Z
  • Filing Date: 2024-12-20T00:00:00.000Z
  • Examiner Employee Number: 95271
  • Art Unit: 1681
  • Tech Center: 1600

Rejection Summary

  • 102 Rejections: 1
  • 103 Rejections: 2

Cited Patents

No patents were cited in this rejection.

Office Action Text


    DETAILED ACTION
Notice of Pre-AIA  or AIA  Status
The present application is being examined under the pre-AIA  first to invent provisions. 

Response to Restriction/Election Requirement
The Response to Election of Species filed April 2, 2025 has been entered.

Election/Restrictions
Applicant’s election without traverse of the following species in the reply filed April 2, 2025 is acknowledged.
Wherein the first and second detectable labels are first and second fluorescent labels, and wherein said plurality of signal signatures comprises at least one signal signature associated with no fluorescent color, as recited in claims 35 and 50, and wherein the first and second fluorescent colors are the same color, as recited in claims 36 and 51.
Wherein said cell or tissue sample is a plurality of fixed cells immobilized on a solid support, as recited in claim 40.
Wherein said first and second fluorescent labels are attached to said first and second decoder probes indirectly via a non-covalent bond, as recited in claims 43 and 54; and 
Removing said first signal sequence by removing said first decoder probe, as recited in claims 47 and 60.
Claims 34, 37, 41-42, 44-46, 49, 52-53, 55-56 and 59 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on April 2, 2025.

Information Disclosure Statements
Each of the seven Information Disclosure Statements submitted December 20, 2024 has been considered. In addition, the Information Disclosure Statements submitted March 11, 2025 and April 2, 2025 have been considered.

Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES

Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.

Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 - 1.825.

Specifically, the specification includes SEQ ID NOs: 1-82. However, only SEQ ID NO: 1 appears in the sequence listing submitted December 20, 2024. A replacement sequence listing which includes all 82 sequences must be provided.

Required response – Applicant must provide:
A "Sequence Listing" part of the disclosure, as described above in item 1); as well as
An amendment specifically directing entry of the "Sequence Listing" part of the disclosure into the application in accordance with 1.825(b)(2); 
A statement that the "Sequence Listing" includes no new matter in accordance with 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide: 
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of: 
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); 
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter; 
If the "Sequence Listing" part of the disclosure is submitted according to item 1) b), c), or d) above, Applicant must also provide: 
A replacement CRF in accordance with 1.825(b)(6); and
Statement according to item 2) a) or b) above. 

Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.

Specifically, the incorporation by reference paragraph describes the size of the XML file in kilobytes. However, it must be listed in bytes, not kilobytes.

Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); 
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter. 


Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA  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 –

(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.


Claims 31-32 and 38-40 are rejected under pre-AIA  35 U.S.C. 102(a)(1) as being anticipated by Geiss1 (WO 2007/076128 A2).

Regarding independent claim 31, Geiss teaches …
A method, comprising: (a) contacting a cell or tissue sample comprising an analyte with 
a detection reagent to bind said detection reagent to said analyte in said cell or tissue sample (Figs. 3A-3B; p. 16, ll. 21-32; p. 21, ll. 15-30); 
wherein said detection reagent comprises (i) a probe that binds to said analyte and (ii) one or more predetermined subsequences (Figs. 3A-3B; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 21, ll. 15-30);
and (b) detecting said one or more predetermined subsequences in said cell or tissue sample in a temporally sequential manner to obtain a plurality of signal signatures associated with said analyte (Figs. 3A-3B; Figs. 5A-5D: individual images were taken at different wavelengths, and then superimposed, thus the images were obtained in a temporally sequential manner; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 21, ll. 15-30; p. 76, ll. 27-31; p. 123, ll. 10-15).

Regarding dependent claim 32, Geiss additionally teaches a plurality of predetermined sequences (Figs. 3A-3B; p. 20, ll. 1-11). 

Regarding dependent claims 38-39, Geiss additionally teaches at least five or at least 10 signal signatures, as recited in claims 38-39, respectively (Figs. 1A-1F; p. 15, ll. 26-32 through p. 16, l. 1-10: Fig. 1A utilizes a 16-position nanoreporter code, where each position can be labeled with one of four types of label monomers).

Regarding dependent claim 40, Geiss additionally teaches that the cell or tissue sample is a plurality of fixed cells immobilized on a solid support (p. 50, ll. 10-15; p. 53, ll. 30-32 through p. 54, ll. 1-2; p 54, ll. 21-24; p. 82, ll. 15-30).

Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA  35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA  35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary.  Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA  35 U.S.C. 103(c) and potential pre-AIA  35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA  35 U.S.C. 103(a).

Claims 33, 35-36, 43 and 47 are rejected under pre-AIA  35 U.S.C. 103(a) as being unpatentable over Geiss (WO 2007/076128 A2) as applied to claims 31-32 above, and further in view of Schubert (Analyzing proteome topology and function by automated multidimensional fluorescence microscopy, Nature Biotechnology, 24(10), pp. 1-9, 2006).

Regarding dependent claims 33 and 47, Geiss teaches that detecting said plurality of 
predetermined subsequences in said cell or tissue sample in said temporally sequential manner comprises: (i) binding a first detectable moiety to a first predetermined sequence of said plurality of predetermined subsequences, wherein said first detectable moiety comprises a first detectable label; (ii) detecting said first detectable label to obtain a first signal signature of said plurality of signal signatures; (iv) binding a second detectable moiety to a second predetermined sequence of said plurality of predetermined subsequences, wherein said second detectable moiety comprises a second detectable label; and (v) detecting said second detectable label to obtain a second signal signature of said plurality of signal signatures (Figs. 3A-3B; Figs. 5A-5D; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 21, ll. 15-30; p. 76, ll. 27-31; p. 123, ll. 10-15).

Geiss does not teach that the detectable moiety is indirectly attached to the predetermined sequence via a decoder probe. Geiss also does not teach … (iii) removing said first signal signature from said cell or tissue sample. However, Schubert teaches these limitations. Specifically, Schubert teaches using a plurality of fluorescent dyes attached to a plurality affinity reagents (i.e., decoder probes) to label the target. Schubert further teaches that each round of detection uses an individual affinity reagent and that after imaging, each fluorescent dye is removed, in part, by washing before adding another affinity reagent (p. 1, left col., para. 3 through right col., para. 2; p. 8, left col., para. 3: “a pair of antibodies was added … images were acquired … the sample was washed with PBS”; Figs. 1-7).

Prior to the date of the instant invention, it would have been prima facie obvious to modify the Geiss method with the Schubert probe. The ordinary artisan would have had the expectation that substituting the Geiss method with removable and replaceable labels would result in a more efficient and flexible method, as it would increase the combinatorial complexity of the Geiss method. The ordinary artisan would have had an expectation of success as the design and modification of detection techniques is well-known in the art.

Regarding dependent claims 35-36, Geiss teaches that the first and second detectable labels are first and second fluorescent labels, which correspond to first and second signal signatures, and that at least one signal signature is associated with no fluorescent color, as recited in claim 35. Geiss also teaches that the first and second fluorescent colors are the same color, as recited in claim 36 (Figs. 3A-3B; p. 21, ll. 15-30; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 43, ll. 31-33 through p. 44, ll. 1-15).

Regarding dependent claim 43, Geiss additionally teaches that the fluorescent labels are indirectly attached to the decoder probes via a non-covalent bond (p. 27, ll. 20-25). 

Claims 48, 50-51, 54, 57-58 and 60 are rejected under pre-AIA  35 U.S.C. 103(a) as being unpatentable over Geiss (WO 2007/076128 A2) in view of Schubert (Analyzing proteome topology and function by automated multidimensional fluorescence microscopy, Nature Biotechnology, 24(10), pp. 1-9, 2006).

Regarding independent claim 48, Geiss teaches …
A method, comprising: (a) providing a cell or tissue sample, wherein said cell or tissue 
sample comprises a ribonucleic acid (RNA) analyte (Figs. 3A-3B; p. 82, ll. 15-30);
(b) contacting said cell or tissue sample with a detection reagent to bind said detection reagent to said RNA analyte at said spatial location, wherein said detection reagent is a nucleic acid molecule comprising: (i) a probe sequence that hybridizes to said RNA analyte and (ii) a plurality of predetermined subsequences (Figs. 3A-3B; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 21, ll. 15-30);
and (c) detecting said plurality of predetermined sequences in said cell or tissue sample in a temporally sequential manner to obtain a plurality of signal signatures at said spatial location (Figs. 3A-3B; Figs. 5A-5D: individual images were taken at different wavelengths, and then superimposed, thus the images were obtained in a temporally sequential manner; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 21, ll. 15-30; p. 76, ll. 27-31; p. 123, ll. 10-15);
wherein said detecting comprises: (i) contacting said cell or tissue sample with a first detectable moiety to bind said first detectable moiety to a first predetermined subsequence of said plurality of predetermined subsequences, wherein said first decoder probe comprises a first detectable label; (ii) detecting said first detectable label to obtain a first signal signature of said plurality of signal signatures at said spatial location; (iv) contacting said cell or tissue sample with a second detectable moiety to bind said second detectable moiety to a second predetermined subsequence of said plurality of predetermined subsequences, wherein said second detectable moiety comprises a second detectable label; and (v) detecting said second detectable label to obtain a second signal signature of said plurality of signal signatures at said spatial location (Figs. 3A-3B; Figs. 5A-5D; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 21, ll. 15-30; p. 76, ll. 27-31; p. 123, ll. 10-15).

Geiss does not teach that the sample is attached to a solid support, or that the 
analyte is at a spatial location of said cell or tissue sample. However, Schubert teaches these limitations. Specifically, Schubert teaches tissue sections attached to a slide (i.e., a solid support) (p. 8, left col., para. 2), and that the method preserves the in situ localization of the analyte (abstract, Fig. 2).

Geiss does not teach that the detectable moiety is indirectly attached to the predetermined sequence via a decoder probe. Geiss also does not teach … (iii) removing said first signal signature from said cell or tissue sample. However, Schubert teaches these limitations. Specifically, Schubert teaches using a plurality of fluorescent dyes attached to a plurality affinity reagents (i.e., decoder probes) to label the target. Schubert further teaches that each round of detection uses an individual affinity reagent and that after imaging, each fluorescent dye is removed, in part, by washing before adding another affinity reagent (p. 1, left col., para. 3 through right col., para. 2; p. 8, left col., para. 3: “a pair of antibodies was added … images were acquired … the sample was washed with PBS”; Figs. 1-7).

Prior to the date of the instant invention, it would have been prima facie obvious to modify the Geiss method with the Schubert probe. The ordinary artisan would have had the expectation that substituting the Geiss method with removable and replaceable labels would result in a more efficient and flexible method, as it would increase the combinatorial complexity of the Geiss method. The ordinary artisan would have been further motivated to modify the Geiss method with the sample preparation steps of Schubert as Schubert teaches that it is desirable to preserve the in situ localization of analytes (abstract). The ordinary artisan would have had an expectation of success as the design and modification of sample preparation techniques are well-known in the art.


Regarding dependent claims 50-51, Geiss teaches that the first and second detectable labels are first and second fluorescent labels, which correspond to first and second signal signatures, and that at least one signal signature is associated with no fluorescent color, as recited in claim 50. Geiss also teaches that the first and second fluorescent colors are the same color, as recited in claim 51 (Figs. 3A-3B; p. 21, ll. 15-30; p. 16, ll. 21-32; p. 20, ll. 1-11; p. 43, ll. 31-33 through p. 44, ll. 1-15).

Regarding dependent claim 54, Geiss additionally teaches that the fluorescent labels are indirectly attached to the decoder probes via a non-covalent bond (p. 27, ll. 20-25). 

Regarding dependent claims 57-58, Geiss additionally teaches at least five or at least 10 signal signatures, as recited in claims 57-58, respectively (Figs. 1A-1F; p. 15, ll. 26-32 through p. 16, l. 1-10: Fig. 1A utilizes a 16-position nanoreporter code, where each position can be labeled with one of four types of label monomers).

	Regarding dependent claim 60, Geiss also does not teach removing said first decoder probe by washing. However, Schubert teaches this limitation. Specifically, Schubert teaches using a plurality of fluorescent dyes attached to a plurality affinity reagents (i.e., decoder probes) to label the target. Schubert further teaches that each round of detection uses an individual affinity reagent and that after imaging, each fluorescent dye is removed, in part, by washing before adding another affinity reagent (p. 1, left col., para. 3 through right col., para. 2; p. 8, left col., para. 3: “a pair of antibodies was added … images were acquired … the sample was washed with PBS”; Figs. 1-7).

Prior to the date of the instant invention, it would have been prima facie obvious to further modify the modified Geiss method, discussed above, with the Schubert washing step. The ordinary artisan would have had the expectation that substituting the Geiss method with a step to remove the labels would result in a more efficient and flexible method, as it would allow removing and replacing labels which would increase the combinatorial complexity of the Geiss method. The ordinary artisan would have had an expectation of success as the design and modification of detection techniques is well-known in the art.

Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA  as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b). 
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.

Claims 31-33, 35-36 38-40, 43, 47-48, 50-51, 54, 57-58 and 60 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-70 of U.S. Patent No. 11,639,518. 

Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of US Patent No. 11,639,518 represent a narrower species of the current claims, and this species anticipates the current, more generic claims. Both sets of claims are drawn to methods for identifying an analyte, including RNA analytes, in a cell or tissue sample comprising the steps of contacting the cell or tissue with a detection reagent comprising a probe that bind to the analyte and at least one predetermined sequence that identifies the analyte, wherein the cell or tissue sample is on a solid support (see claims 22 and 42 of the ‘518 patent), sequencing the at least one predetermined sequence in a temporally sequential manner to detect a plurality of signal signatures in the cell or tissue sample (see claim 31 of the ‘518 patent) which teaches using decoder probes to associate at least one optical label with the predetermined sequences), wherein the plurality of optical signal signatures comprise at least one signal signature of no color (see claims 10 and 29 of the ‘518 patent), and using a temporal order of the plurality of signal signatures to identify the analyte in the cell or tissue sample. In addition, the claims of the ‘518 patent also teach that the method comprises identifying an analyte at a spatial location in the cell or tissue sample, wherein a temporal order of the plurality of optical signal signatures at a spatial location is used to identify the analyte at the spatial location. 

Claims 31-33, 35-36 38-40, 43, 47-48, 50-51, 54, 57-58 and 60 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,566,277. 

Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of US Patent No. 11,566,277 represent a narrower species of the current claims, and this species anticipates the current, more generic claims. Both sets of claims are drawn to methods for identifying an analyte, including RNA analytes, in a cell or tissue sample comprising the steps of contacting the cell or tissue with a detection reagent comprising a probe that bind to the analyte and at least one predetermined sequence that identifies the analyte, wherein the cell or tissue sample is on a solid support (see claim 28 of the ‘277 patent), sequencing the at least one predetermined sequence in a temporally sequential manner to detect a plurality of signal signatures in the cell or tissue sample (see claims 6, 15 and 18 of the ‘277 patent which teach using decoder probes to associate at least one optical label with the predetermined sequences), wherein the plurality of signal signatures comprise at least one signal signature of no color (see claims 7 and 14 of the ‘277 patent), and using a temporal order of the plurality of signal signatures to identify the analyte in the cell or tissue sample. In addition, the claims of the ‘277 patent also teach that the method comprises identifying an analyte at a spatial location in the cell or tissue sample, wherein a temporal order of the plurality of optical signal signatures at a spatial location is used to identify the analyte at the spatial location. 

Claims 31-33, 35-36 38-40, 43, 47-48, 50-51, 54, 57-58 and 60 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-82 of U.S. Patent No. 11,293,052. 

Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of US Patent No. 11,293,052 represent a narrower species of the current claims, and this species anticipates the current, more generic claims. Both sets of claims are drawn to methods for identifying an analyte, including RNA analytes, in a cell or tissue sample (see claim 46 of the ‘052 patent) comprising the steps of contacting the cell or tissue with a detection reagent comprising a probe that bind to the analyte and at least one predetermined sequence that identifies the analyte (see claim 2 of the ‘052 patent), wherein the cell or tissue sample is on a solid support (see claim 47 of the ‘052 patent), sequencing the at least one predetermined sequence in a temporally sequential manner to detect a plurality of signal signatures in the cell or tissue sample (see claims 2-5 of the ‘052 patent which teach using decoder probes to associate at least one optical label with the predetermined sequences), wherein the plurality of signal signatures comprise at least one signal signature of no color, and using a temporal order of the plurality of signal signatures to identify the analyte in the cell or tissue sample. In addition, the claims of the ‘052 patent also teach performing three or more readout cycles to generate the temporal order of signal signatures by detecting optical signals associated with the nucleic acid labels of the detection reagent (predetermined sequences). 

Claims 31-33, 35-36 38-40, 43, 47-48, 50-51, 54, 57-58 and 60 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,976,318. 

Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of US Patent No. 11,976,318 represent a narrower species of the current claims, and this species anticipates the current, more generic claims. Both sets of claims are drawn to methods for identifying an analyte, including RNA analytes, in a cell or tissue sample comprising the steps of contacting the cell or tissue with a detection reagent comprising a probe that bind to the analyte and at least one predetermined sequence that identifies the analyte, wherein the cell or tissue sample is on a solid support, sequencing the at least one predetermined sequence in a temporally sequential manner to detect a plurality of signal signatures in the cell or tissue sample, wherein the plurality of signal signatures comprise at least one signal signature of no color, and using a temporal order of the plurality of signal signatures to identify the analyte in the cell or tissue sample. In addition, the claims of the ‘318 patent also teach performing three or more readout cycles to generate the temporal order of signal signatures by detecting optical signals associated with the nucleic acid labels of the detection reagent (predetermined sequences). 


Conclusion
Claims 31-33, 35-36 38-40, 43, 47-48, 50-51, 54, 57-58 and 60 are being examined, and are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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, Gary Benzion can be reached at 571-272-0782. 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.





/CAROLYN L GREENE/Examiner, Art Unit 1681                                                                                                                                                                                                        


    
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
        
            
    

    
        1 Geiss was cited in the Information Disclosure Statement submitted December 20, 2024.


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