DETAILED ACTION
Status of the Claims
Claims 1-20 are currently pending and are examined herein.
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 14 and 20 are objected to because of the following informalities: claims 14 and 20 do not end with a period. As per MPEP 608.01(m), each claim must begin with a capital letter and end with a period.
Claim Rejections – 35 U.S.C. 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 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.
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.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Ramachandran et al.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Ramachandran et al. (U.S. PGPub 2022/0112486 A1)
Regarding claim 1, Ramachandran discloses a system comprising:
a first body comprising a first subset of molecules and a second subset of molecules coupled to the first body (e.g., as per Fig. 26 and the Examples), wherein a first molecule of the first subset of molecules comprises:
a capture probe configured to capture an analyte of a sample (e.g., capture domain as per Fig. 26 and para [1369]-[1370]), and
wherein a second molecule of the second subset of molecules comprises:
a linker region (e.g., as per Fig. 26 and para [1369]-[1370]), a first particle identification segment unique to the first body (e.g., the spatial barcode and/or UMI as per Fig. 26 and the Examples), and a first active segment positioned at a second terminal end of the second molecule (e.g., as per Fig. 26 and para [1369]-[1370]);
and a second body comprising: a second particle identification segment unique to the second body, and a second active segment configured to interact with the first active segment of the first body (e.g., as shown in Figs. 27 & 28).
However, Ramachanran does not explicitly teach the limitation that the linker is “configured to extend the second molecule into space beyond a first terminal end of the first molecule”, as set forth in claims 1 and 16. Specifically, Ramachandran is silent regarding the relative lengths of the first and second molecules. Fig. 26 of Ramachandran depicts a body with two molecules. These molecules each have a “functional domain/sequence” (e.g., 2605 and 2610), “spatial barcode” (e.g., 2604 and 2609), “UMI” (e.g., 2603 and 2608) that are analogous between the two molecules. Said molecules primarily differ by the presence of a “capture domain” (e.g., 2067) and a “constant sequence” (e.g., 2602). Ramachandran discloses that the “capture domain” includes at least 10-35 nucleotides (e.g., as per para [0344]) and discusses that the “constant sequence” can be “about 15 to about 30 nucleotides long” (e.g., as per para [1140]). In accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists. It is further noted that the present specification discusses the linker region used to “extend the second molecule into space beyond a first terminal end of the first molecule” is done so to enable interactions of the active segments of second subsets of molecules with active segments of neighboring objects (e.g., at paras [0056], [0058]-[0059], and [0094]). It is noted that the teachings of Ramachandran enable the interaction of analogous segments, as depicted in Fig. 27 & 28.
Regarding claim 2, Ramachandran discloses the above system, wherein the capture probe is configured to capture a polyA sequence of a messenger ribonucleic acid molecule (mRNA) molecule (e.g., as per para [0342]).
Regarding claims 3-5 and 11, which require that the analyte is a target analyte is located within a cell is from a surface of a sample, and/or the sample is a tissue sample, and/or wherein the first body and the second body are dispersed within the suspension, it is noted that as per MPEP § 2115, “[i]nclusion of material or article worked upon by a structure being claimed does not impart patentability to the claims.” In re Young, 75 F.2d 996, 25 USPQ 69 (CCPA 1935) (as restated in In re Otto, 312 F.2d 937, 136 USPQ 458, 459 (CCPA 1963)).
Regarding claim 6, Ramachandran discloses the above system, wherein at least one of the first molecule and the second molecule further comprises a cleavable molecule responsive to cleavage by a photocleaving mechanism (e.g., as per para [057]-[0367]).
Regarding claim 7, Ramachandran discloses the above system, wherein the second active segment is configured to interact with the first active segment by hybridization (e.g., as per Fig. 28).
Regarding claim 8, Ramachandran discloses the above system, wherein the second active segment is configured to interact with the first active segment by ligation (e.g., as per Fig. 27).
Regarding claim 9, Ramachandran discloses the above system, wherein the first active segment is structured to preferentially interact with the second active segment and prevent self-interactions with the first active segment (e.g., as per Fig. 28).
Regarding claim 10, Ramachandran discloses the above system, further comprising a substrate retaining the first body and the second body in position (e.g., as per Fig. 29).
Regarding claim 12, Ramachandran discloses the above system, further comprising a film containing the first body and the second body (e.g., as per para [0460]).
Regarding claim 13, Ramachandran discloses the above system, wherein the first particle identification segment comprises a first random sequence and wherein the second particle identification segment comprises a second random sequence (e.g., UMIs as per [1369]).
Regarding claim 14, Ramachandran discloses the above system, wherein the first subset of molecules of the first body provides at least 300 functional sites for capture of analytes from the sample (e.g., “Each bead can be covered with hundreds of thousands of copies of a specific oligonucleotide” as per para. [0626]).
Regarding claim 15, Ramachandran discloses a method comprising:
positioning a first body and a second body in proximity to a sample comprising a set of targets; capturing a first target of the set of targets by a first capture probe coupled to the first body; capturing a second target of the set of targets by a second capture probe coupled to the second body; promoting interactions between a first active segment of the first body and a second active segment of the second body (e.g., as per Figs. 26-29 and the Examples);
identifying a connection between the first body and the second body upon sequencing molecules derived from the first active segment and the second active segment; associating the first body with the first target, and the second body with the second target; and generating a map of relative positioning of the first target and the second target, based upon the connection between the first body and the second body (e.g., as per Fig. 29 and [1373]).
Regarding claim 16, Ramachandran discloses the above method, wherein the first body comprises a first molecule comprising the first capture probe at a first terminal end of the first molecule, and a second molecule comprising a linker region, and a first particle identification segment unique to the first body, wherein the first active segment is positioned at a second terminal end of the second molecule (e.g., as per Figs. 26-29 and the Examples).
Regarding claim 17, Ramachandran discloses the above method, wherein at least one of the first molecule and the second molecule further comprises a cleavable molecule responsive to cleavage by a photocleaving mechanism (e.g., as per para [057]-[0367]).
Regarding claim 18, Ramachandran discloses the above method, wherein the set of targets comprise mRNA molecules of the sample, wherein the first capture probe is configured to capture a polyA sequence of the first target, and wherein the second capture probe is configured to capture a polyA sequence of the second target (e.g., as per para [0342]).
Regarding claim 19, Ramachandran discloses the above method, wherein the first target and the second target are located within a cell (e.g., permeabilizing samples to allow probes to enter as per paras. [0263]-[0273]).
Regarding claim 20, Ramachandran discloses the above method, wherein the first active segment is configured to interact with the second active segment by hybridization (e.g., as per Fig. 28).
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 obviousness-type 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); and 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 a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
U.S. 11,624,088 B2
Claims 1-5, 7-8, and 10-11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 11,624,088 B2 (the ‘088 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, The claims of the ‘088 patent disclose a system comprising:
a first body comprising a first subset of molecules and a second subset of molecules coupled to the first body, wherein a first molecule of the first subset of molecules comprises:
a capture probe configured to capture an analyte of a sample, and
wherein a second molecule of the second subset of molecules comprises:
a linker region configured to extend the second molecule into space beyond a first terminal end of the first molecule, a first particle identification segment unique to the first body, and
a first active segment positioned at a second terminal end of the second molecule;
and a second body comprising: a second particle identification segment unique to the second body, and a second active segment configured to interact with the first active segment of the first body (e.g., as per claim 1 of the ‘088 patent).
Regarding claim 2, The claims of the ‘088 patent disclose the above system, wherein the capture probe is configured to capture a polyA sequence of a messenger ribonucleic acid molecule (mRNA) molecule (e.g., as per claim 3 of the ‘088 patent).
Regarding claims 3-5 and 11, which require that the analyte is a target analyte is located within a cell is from a surface of a sample, and/or the sample is a tissue sample, and/or wherein the first body and the second body are dispersed within the suspension, it is noted that as per MPEP § 2115, “[i]nclusion of material or article worked upon by a structure being claimed does not impart patentability to the claims.” In re Young, 75 F.2d 996, 25 USPQ 69 (CCPA 1935) (as restated in In re Otto, 312 F.2d 937, 136 USPQ 458, 459 (CCPA 1963)).
Regarding claim 7, The claims of the ‘088 patent disclose the above system, wherein the second active segment is configured to interact with the first active segment by hybridization (e.g., as per claim 5 of the ‘088 patent).
Regarding claim 8, The claims of the ‘088 patent disclose the above system, wherein the second active segment is configured to interact with the first active segment by ligation (e.g., as per claims 6-7 of the ‘088 patent).
Regarding claim 10, The claims of the ‘088 patent disclose the above system, further comprising a substrate retaining the first body and the second body in position (e.g., as per claim 8 of the ‘088 patent).
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684
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