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 .
Drawings
The drawings were received on 25 August 2025. These drawings are acceptable.
Claim Interpretation
Attention is directed to MPEP 904.01 [R-08.2012].
The breadth of the claims in the application should always be carefully noted; that is, the examiner should be fully aware of what the claims do not call for, as well as what they do require. During patent examination, the claims are given the broadest reasonable interpretation consistent with the specification. See In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis.
It is noted with particularity that narrowing limitations found in the specification cannot be inferred in the claims where the elements not set forth in the claims are linchpin of patentability. In re Philips Industries v. State Stove & Mfg. Co, Inc., 186 USPQ 458 (CA6 1975). While the claims are to be interpreted in light of the specification, it does not follow that limitations from the specification may be read into the claims. On the contrary, claims must be interpreted as broadly as their terms reasonably allow. See Ex parte Oetiker, 23 USPQ2d 1641 (BPAI, 1992). In added support of this position, attention is directed to MPEP 2111 [R-11.2013], where, citing In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969), is stated:
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.
Additionally, attention is directed to MPEP 2111.01 [R-01.2024], wherein is stated:
II. IT IS IMPROPER TO IMPORT CLAIM LIMITATIONS FROM THE SPECIFICATION
“Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment.” Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).
Attention is also directed to MPEP 2111.02 II [R-07.2022]. As stated herein:
II. PREAMBLE STATEMENTS RECITING PURPOSE OR INTENDED USE
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The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation")… (Emphasis added)
Attention is directed to MPEP 2111 [R-10.2019]. As stated therein:
During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added).
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 106, 108, 109, 112, 117, 118, and 123 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 11-13, 18, 20, 22, and 30 of U.S. Patent No. 11,959,130 B2 (Galonska et al.) in view of US 2008/0050780 A1 (Lee et al.).
Although the claims at issue are not identical, they are not patentably distinct from each other because the claims are to “a method of determining presence of a genetic variant in a nucleic acid at a spatial location in a biological sample”. As seen in claim 1 of the Galonska et al., one uses first and second probes.
Galonska et al., in claims 11-13 teaches using a ligase so to produce a ligation product.
Galonska et al., in claim 18, identifies polymerases that can be used.
As can be seen in dependent claim 20 of Galonska et al., “the biological sample is a tissue section”. In claim 21, the different types of “tissue section” are listed.
Galonska et al., in claims 22 and 23 teach of the nucleic acid being DNA or RNA.
Galonska et al., have not been found to teach incorporating “a single reversible terminator nucleotide” into the first probe.
Lee et al., in their abstract, teach:
Disclosed herein a reversible terminator nucleotides and methods of use. (Emphasis added)
In view of the above showing, it would have been obvious to one of ordinary skill in the art to have incorporated a reversible blocking group to a first probe as such would allow the artisan to determine when the two probes can be ligated, which in turn would go to increase the accuracy of the assay, and the capability of detecting SNPs.
In view of the above showing and in the absence of convincing evidence to the contrary, claims 106, 108, 109, 112, 117, 118, and 123 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 11-13, 18, 20, 22, and 30 of U.S. Patent No. 11,959,130 B2 (Galonska et al.) in view of US 2008/0050780 A1 (Lee et al.).
Claim 106 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,608,520 (Galonska et al.) in view of Lee et al., (US 2008/0050780, Pub. Date 02/28/2008).
Notes: Application 17/552, 980 by Galonska et al. was published as US 2022/016632 A1, and became U.S. Patent No. 11,608,520 (Date of Patent: 03/21/2023).
Claim 1 of U.S. Patent No. 11,608,520 is copied below.
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Galonska et al., have not been found to teach incorporating “a single reversible terminator nucleotide” into the first probe.
Lee et al., in their abstract, teach:
Disclosed herein a reversible terminator nucleotides and methods of use. (Emphasis added)
In view of the above showing, it would have been obvious to one of ordinary skill in the art to have incorporated a reversible blocking group to a first probe as such would allow the artisan to determine when the two probes can be ligated, which in turn would go to increase the accuracy of the assay, and the capability of detecting SNPs.
In view of the above presentation and in the absence of convincing evidence to the contrary, claim 106 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,608,520 (Galonska et al.) in view of Lee et al., (US 2008/0050780, Pub. Date 02/28/2008).
It is noted that essentially the same claim languages have been allowed in (i) U.S. Patent No. 11,608,520, which is Application 17/552, 980 by Galonska et al. US 2022/016632 A1, Pub Date: 04/07/2022, Applicant’s own prior art (10X Genomics) published more than one year before the effective filing date 08/24/2023 of instant application 19/087,021; and (ii) U.S. Patent No. 11,959,130, which is Application 18/179,795 by Galonska et al. was published as US 2023/0220455 A1, Pub. Date 07/13/2023, also Applicant’s own prior art published before the effective filing date 08/24/2023 of instant application 19/087,021.
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) 106, 108, 109, 112, 117, 118, and 123 is/are rejected under 35 U.S.C. 103 as being unpatentable over Galonska et al. (US 2022/0106632 A1, Pub. Date 04/07/2022, filed on 12/15/2021; application 17/551,980) in view of Lee et al. (US 2008/0050780, Pub. Date 02/28/2028) .
Galonska et al., in claims 109, 126, and 128 teach:
109. A method for determining the presence or absence of a genetic variant in an analyte at a spatial location in a biological sample on a substrate, the method comprising:
(a) contacting the biological sample with a first probe and a second probe, wherein the first probe and the second probe each comprise a sequence that is substantially complementary to sequences of the analyte, wherein the first probe and the second probe are capable of forming an invasive cleavage structure in the presence of the genetic variant, and wherein:
(i) the first probe further comprises at least one nucleotide that is complementary to a wild-type sequence of the genetic variant; and
(ii) the second probe further comprises:
a sequence of non-complementary nucleotides;
a nucleotide complementary to the genetic variant; and
a capture probe binding domain;
(b) hybridizing the first probe and the second probe to the analyte;
(c) cleaving the sequence of non-complementary nucleotides when the genetic variant is present;
(d) ligating the first probe and the second probe, thereby creating a ligated probe; (e) releasing the ligated probe from the analyte;
(f) contacting the ligated probe with a substrate comprising a plurality of capture probes, wherein a capture probe of the plurality comprises a spatial barcode and the capture domain;
(g) hybridizing the ligated probe to the capture domain; and
(h) determining (i) all or a part of the sequence of the ligated probe specifically bound to the capture domain, or a complement thereof, and (ii) all or a part of the sequence of the spatial barcode, or a complement thereof, and using the determined sequence of (i) and (ii) to determine the presence or absence of a genetic variant in an analyte in a spatial location in the biological sample on the substrate. (Emphasis added)
126. The method of claim 109, wherein the biological sample is a tissue section.
128. The method of claim 109, wherein the analyte is RNA or DNA.
As evidenced above, Galonska et al., teach and claim a method of determining if a genetic variant is present or not in a biological sample, which, as seen in claim 126 is a tissue section. As set forth in claim 128, the analyte is RNA.
Galonska et al., teach:
[0034) Also disclosed herein are kits. In some instances, the disclosure provides a kit comprising: (a) an array comprising a plurality of capture probes; (b) a plurality of probes comprising a first probe oligonucleotide and a second probe oligonucleotide, wherein the first probe oligonucleotide and the second probe oligonucleotide each comprise a sequence that is substantially complementary to adjacent sequences of the analyte, wherein the first probe oligonucleotide and the second probe oligonucleotide are capable of forming an invasive cleavage structure in the presence of the analyte, wherein the second probe oligonucleotide comprises a capture probe binding domain; and (c) instructions for performing any of the methods disclosed herein.
[0035) In some instances, the disclosure provides a kit comprising: (a) an array comprising a plurality of capture probes; (b) a plurality of probes comprising a first probe oligonucleotide and a second probe oligonucleotide, wherein the first probe oligonucleotide and the second probe oligonucleotide each comprise a sequence that is substantially complementary to sequences of the analyte where there is a gap between the sequences of the analyte, wherein the first probe oligonucleotide and the second probe oligonucleotide are capable of forming an invasive cleavage structure in the presence of the analyte, wherein the second probe oligonucleotide comprises a capture probe binding domain; and (c) instructions for performing any of the methods disclosed herein.
[0027] In some instances, the method further comprises providing a capture probe binding domain blocking moiety that interacts with the capture probe binding domain. In some instances, the method further comprises releasing the capture probe binding domain blocking moiety from the capture probe binding domain prior to contacting the biological sample with the substrate.
Galonska et al. (US 2022/0106632) does not explicitly teach the limitation “a single reversible terminator Nucleotide” recited in step (c) and the limitation “removing the blocking group from the reversible terminator nucleotide” recited in step (f) of claim 106 of instant application 19/087,021.
Lee et al. (US 2008/0050780) teaches a reversible terminator nucleotides and
methods of use (See Abstract, Title, and Figure 1).
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[0002] Methods of polynucleotide sequencing that employ reversible terminator nucleotides typically involve multiple steps to identify a single base and to regenerate a 3' terminus of the sequencing primer which is required permit identification of each succeeding base of the polynucleotide. These steps typically include incorporation of a reversible terminator at the 3' terminus of the primer, washing away the unincorporated reversible terminators and other sequencing reagents, detection of the label attached to the incorporated reversible terminator, removal of the label from the incorporated terminator, and removal of blocking group from the reversible terminator. Therefore, current methods of polynucleotide sequencing using reversible terminators are time-consuming, labor intensive, and have a high-cost associated with the identification of each base. Therefore, there is a need in the art for reversible terminator nucleotides and methods of use that reduce the number of steps required for the identification of each base of a polynucleotide.
[0007] Disclosed herein are compositions and methods for sequencing polynucleotides, including single-molecule sequencing. The compositions disclosed herein include reversible terminator nucleotides that can be incorporated at the 3' terminus of a polynucleotide by a polymerase in a template dependent/directed manner. In some embodiments, the reversible terminator nucleotides generally include a hydroxyl group at the 3'-position of a sugar moiety, a blocking group at the 2'-position of the sugar moiety, and a label attached to the base. Upon incorporation of a reversible terminator nucleotide, the blocking group renders the polynucleotide non-extendible by the polymerase. In some embodiments, the incorporated reversible terminators also are generally resistant to 3'-5' exonucleases or "proofreading activities" of polymerases.
In view of the above presentation, it would have been quite obvious to one of ordinary skill in the art at the time of the invention to have incorporated reversible terminator nucleotides into the probe/primer for to do so would enhance the artisan to determine the nucleotide sequence beyond that of just where the probe anneals/hybridizes to the genetic sequence in the tissue sample.
In view of the well developed state of the art said ordinary artisan would have been amply motivated and would have had a most reasonable expectation of success in being able to determine the presence of a genetic in a tissue sample.
In view of the above presentation and in the absence of convincing argument to the contrary, claims 106, 108, 109, 112, 117, 118, and 123 is/are rejected under 35 U.S.C. 103 as being unpatentable over Galonska et al. (US 2022/0106632 A1, Pub. Date 04/07/2022, filed on 12/15/2021; application 17/551,980) in view of Lee et al. (US 2008/0050780, Pub. Date 02/28/2028) .
Conclusion
Objections and/or rejections which appeared in the prior Office action and which have not been repeated hereinabove have been withdrawn.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM..
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, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682