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 .
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 4, 17, 21, and 22 have been canceled. Claims 2-3, 5-16, 18-20, and 23-31 are pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 1/26/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Response to Applicant’s Amendments
Drawings Objections
The drawings were objected to because they included a reference sign not mentioned in the description, and because the specification included a reference character not mentioned in the drawings. In light of Applicant’s newly amended drawings submitted 1/26/2026, these objections have been withdrawn.
Claim Objections
Claims 2-4 and 20-22 were objected to for minor informalities. Claims 4 and 21-22 have been canceled, so these objections have been rendered moot. In light of Applicant’s claim amendments submitted 1/26/2023, the objections for claims 2-3 and 20 have been withdrawn.
35 USC 112(b) Rejections
Claims 2, 5-20, and 23-31 were rejected for various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 1/26/2026, these rejections have been withdrawn for all currently pending claims. Claim 17 has been cancelled, and so this rejection has been rendered moot.
35 USC 103 Rejections
Claims 2-31 were rejected under 35 U.S.C. 103 as being unpatentable over Frisén et al. (WO 2018/091676 A1), in view of Zhu et a. (US 2016/0060687 A1), and in view of Fu et al. (US 2011/0269631 A1). Applicant’s arguments and amendments have been thoroughly reviewed and considered. These rejections have been withdrawn for all currently pending claims, but see “Response to Applicant’s Arguments” and new grounds of rejection below. Claims 4, 17, 21, and 22 have been canceled, and so these rejections have been rendered moot.
Response to Applicant’s Arguments
With regard to the 35 USC 103 Rejections, Applicant argues that in the Non-Final Rejection, the modification to Frisén to hybridize a second probe to the extended first capture probe (as required by step (g) of instant claim 2) would be inconsistent with the intended purpose of Frisén, as the reference recites that the release of their capture probes from the solid substrate can occur simultaneously or subsequently to extension, and such release is allegedly central to the improvements to the art taught by the reference (Remarks, pages 10-11). Thus, the modification would render the reference inoperable for its intended purpose. Additionally, Applicant argues that the proposed modification would render Frisén’s method less effective and/or sensitive and more burdensome, as it would allegedly reduce capture of target nucleic acids and would require more active steps (Remarks, pages 12-13). Finally, Applicant alleges that there is no motivation to combine Frisén with Zhu, and there would be no reasonable expectation of success with such a combination (Remarks, page 13).
With regard to Applicant’s arguments regarding Frisén being rendered inoperable for its intended purpose, Frisén does state that in their invention combining the probe release and extension steps to be performed simultaneously can improve sensitivity (page 2, para. 4 and page 3, para. 1). However, the reference also states that release and extension of the probes may occur sequentially, where extension follows release (Abstract and page 4, para. 1, for example). This release and subsequent extension is only discussed with regard to sensitivity on page 7, para. 2, where mechanisms for increased sensitivity are described in the context of combining release and extension reactions. In fact, with regard to embodiments encompassing subsequent release/extension, the methods may comprise the listed steps, and so other steps may be performed between probe release and extension (e.g. page 4, para. 1). Additionally, page 7, para. 3 notes that simultaneous release and extension “does not mean that all capture probes will be released and extended at the same time, but rather that the means for releasing and extending the capture probes are applied to the solid substrate…simultaneously.” Page 8, para. 3 also states that simultaneous or subsequent release/extension need not apply to all probes on a solid substrate. Page 9, para. 4 states that for release and subsequent extension, this “may be achieved by contacting solid substrate with the means for releasing said capture probes from the surface of the solid substrate and the polymerase enzyme separately.” Page 10, para. 2 notes that subsequent extension can occur up to 72 hours after release from a substrate. For the cDNA synthesis embodiment of Frisén specifically (which is used in the Non-Final Rejection), synthesis and extension of the cDNA is stated to at least partially occur on the substrate (see page 57, para 2 through page 58, para. 3), and thus, in at least one embodiment, probes are extended on the solid support. Thus, while Frisén does discuss benefits associated with simultaneous release/extension of capture probes, it is unclear if these benefits would extend to all versions of release and subsequent extension encompassed by Frisén due to their broad definition. Additionally, as all of the embodiments of the invention do not encompass such release and simultaneous/subsequent extension, this is not considered central to the principle of operation of Frisén .
Furthermore, the intended purpose of Frisén is considered to be spatial tagging of nucleic acids in a biological specimen (as stated in the Abstract and page 1, para. 1 of Frisén). In combining Frisén and Zhu in the Non-Final Rejection, the cDNA methods of Frisén (where extension can occur on the array) are utilized, and the capture probe of Frisén is simply hybridized to another probe on the substrate (see para. 28 of the Non-Final Rejection). The target nucleic acids are still incorporated into the probes along with the positional domain described by Frisén, and so this purpose is still accomplished with this combination.
Thus, this argument is not considered persuasive.
Regarding Applicant’s arguments that the combination of Frisén in view of Zhu would render Frisén’s method less effective and/or sensitive and more burdensome, MPEP 2143.01 I notes that, “The disclosure of desirable alternatives does not necessarily negate a suggestion for modifying the prior art to arrive at the claimed invention. In In re Fulton, 391 F.3d 1195, 73 USPQ2d 1141 (Fed. Cir. 2004),” and MPEP 2143.01 V states that, “[a] given course of action often has simultaneous advantages and disadvantages, and this does not necessarily obviate motivation to combine’" (quoting Medichem, S.A. v. Rolabo, S.L., 437 F.3d 1157, 1165, 77 USPQ2d 1865, 1870 (Fed. Cir. 2006).” In combining Frisén and Zhu, though Applicant may be correct in pointing out potential disadvantages of this combination, there are also advantages associated with said combination that are explained in the Non-Final Rejection (see para. 29) – including increased accuracy and confidence in results. As a proper motivation and reasonable expectation of success for this combination have been provided (see the response to Applicant’s final arguments below), the presence of particular advantages and disadvantages do not obviate the properness of the obviousness rejection.
Thus, this argument is not considered persuasive.
As to Applicant’s arguments against Frisén and Zhu for a lack of motivation to combine, this is addressed by the Non-Final Rejection. Para. 29 states, “The ordinary artisan would thus be motivated to make such a combination of Frisén in view of Zhu because when these double-stranded products are analyzed via amplification and sequencing, the second capture probes that were appropriately hybridized to and amplified will be easily identified via sequencing by the number/order of their sequences present on the reads (e.g. the capture probe sequence with the template switching oligonucleotide sequence, the cDNA equivalent of the mRNA sequence, and the complement of the first capture probe sequence). This would indicate probe sequences that successfully went through all of the intended steps of the method, and would allow for the filtering of the sequence reads to only include appropriate sequences in analyses. This would eliminate erroneous reads and/or would indicate if the method was working as intended. Overall, this would increase the accuracy of the method and the confidence in the results.” Additionally, the Non-Final Rejection contains rationale for a reasonable expectation of success in combining the references. Para. 28 states, “As template-switching methodology is well-known (see Frisén page 60, para. 3) and does not rely on an unknown natural sequence, but instead that of an oligonucleotide probe, and Frisén and Zhu both teach methods of probe design (e.g. Frisén page 32, para. 2 and Zhu para. 328), it would be possible to design the second capture probes with this template-switching oligonucleotide sequence in mind. Zhu notes that probe sequences near each other on a solid support may hybridize to one another to form a coupled product that can be used for downstream analysis, providing a reasonable expectation of success that the same could be done with the hybridized capture probes of Frisén.” Applicant does not appear to directly address these assertions by the Examiner, and instead points out a quotation earlier in para. 28 of the Non-Final Rejection where Frisén and Zhu were noted to have commonalities with one another. These commonalities were noted by the Examiner in order to show that the references both generally deal with methods related to probes, barcoding, and analyte location, providing support that the ordinary artisan would be capable of using the teachings of the references together. These commonalities also provide support that these references are analogous art to the claimed invention (e.g. they are in the same field of endeavor), which is a requirement for an obviousness rejection (See MPEP 2141.01(a) I). Thus, as Applicant has not addressed the specific rationale used by the Examiner in combining these references, their combination is considered proper, and this argument by Applicant is not persuasive.
Additionally, it is noted that Applicant primarily relies on the invention and teachings of Frisén in their arguments, and only briefly mentions the teachings of Zhu while not mentioning the teachings of Fu at all. The rejections of claims 2-31 in the Non-Final Rejection were based on Frisén, in view of Zhu, and in view of Fu, and so Applicant did not fully address the scope of the obviousness rejection. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Thus, overall, Applicant’s arguments are not considered persuasive. The relevant portions of the 35 USC 103 Rejections presented in the Non-Final Rejection have been reiterated below, and new grounds of rejection are presented due to Applicant’s amendments to the claims.
Claim Interpretation
Regarding claims 2 and 20, though the second probe must have a second capture domain that is a template switching oligonucleotide sequence or a partial sequence thereof, it is noted that no actual template switching utilizing this sequence is required. Additionally, a “template switching oligonucleotide sequence” is not defined by the instant specification, and the claim only requires that the second probe contain a “partial sequence” of said template switching oligonucleotide sequence. This would amount to even a single nucleotide in common with a template switching oligonucleotide.
Regarding claims 3 and 20, the use of the phrasing “thereby generating the spatially barcoded extension product” after the recitation of extension will be interpreted as the extension naturally generating the spatially barcoded extension product, with no additional steps being 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.
Claims 2-3, 5-16, 18-20, and 23-31 are rejected under 35 U.S.C. 103 as being unpatentable over Frisén et al. (WO 2018/091676 A1), in view of Zhu et a. (US 2016/0060687 A1), and in view of Fu et al. (US 2011/0269631 A1).
Frisén teaches methods for spatially tagging nucleic acid molecules in a biological specimen (Abstract). This method involves providing a solid substrate with multiple species of capture probes in particular locations, where each probe has a positional domain (which can act as a spatial barcode) and a capture domain. Thus, the reference teaches at least two probes attached to a substrate. The biological specimen is put into contact with the capture probes, and the nucleic acids in the specimen hybridize to the probes. Extension of the probes may then occur (pages 3-4). mRNA may specifically be captured from the biological specimen (page 7, para. 1). The capture domain of the capture probe may be a poly (T) sequence that is designed to bind to the poly (A) tail of the mRNA (page 28, para. 2). After extension, the 3’ end of the extended probe may be further extended in order to initiate second strand cDNA synthesis. Specifically, a reverse transcriptase may add a few nucleotides to the end of the extended cDNA (acting as the claimed untemplated nucleotides; page 60, para. 3). Then, template switching can occur, utilizing an additional oligonucleotide probe (which would be the template switching oligonucleotide) to further extend the cDNA molecule (page 60, para. 3 and page 61, para. 1), creating a second strand. After the double-stranded cDNA is created, unwanted capture probes may be removed (page 61, para. 2). The ordinary artisan would recognize that it would also be obvious to remove other sequences that are no longer or never were hybridized to either strand of the double-stranded cDNA (such as mRNA molecules and the template switching oligonucleotide) to ensure that only desired sequences remain on the solid support. This would ensure the efficiency and accuracy of any downstream methods, such as further amplification and sequencing.
This second strand synthesis can produce a truncated strand of cDNA, meaning each strand of the double-strand would not be the same length (page 61, para. 3). And while Frisén notes that this second strand synthesis may occur on the solid support, the second strand need not be attached to the solid support (page 61, para. 1).
However, Frisén does not teach that a second probe hybridizes to the extended first capture probe as required by step (g) of instant claim 2.
Zhu teaches methods of proximity coupling on substrates, where analytes and binding moieties are analyzed (Abstract). Specifically, the reference teaches two probes, a proximity probe and an address probe, where the two probes are coupled when an analyte is present (para. 6). Each probe has its own barcode sequence and a linker sequence (see Figure 1A for example). The ends of the address and proximity probes may be adjacent to one another (para. 35). Furthermore, the two probes may be hybridized to one another (para. 36). The two probes may be from the same region on the solid support (para. 39). The address polynucleotide is barcoded to a target analyte (para. 268) and is coupled to a solid support (para. 270), particularly at its 5’ end (para. 292). The proximity probe may be hybridized to the address polynucleotide via the use of a linker present at its 3’ end (para. 315). Hybridization of the two probes can occur due to the length of their linker sequences at their free ends (para. 345), and Zhu mentions considering linker sequence nucleotides carefully to prevent unwanted hybridization (para. 346). The hybridized product can then be further amplified/analyzed (para. 354). Zhu teaches various advantages for having two barcode sequences, including quantitative detection and analyte location analysis (para. 355). Sequencing of the hybridized product can also be performed (para. 386).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Zhu within the context of the methods of Frisén to arrive at the method of instant claim 2. Specifically, the extensions of the capture probe of Frisén result in a long probe sequence, containing the initial capture probe sequence, the cDNA complement to the mRNA sequence, untemplated nucleotides, and the complementary sequence to the template switching oligonucleotide. This would extend the length of capture probe greatly, so much so that it would be possible to hybridize the sequence to another probe present on the solid substrate. Zhu teaches hybridizing two probe sequences to one another if a target is present, also utilizes barcode sequences, and has applications for locating particular analytes. These commonalities with Frisén would prompt the ordinary artisan to consider combining the references. Regarding the capture probes of Frisén, the reference states, “it is not required that each member of a species of capture probe has the same sequence in its entirety,” (page 31, para. 4), where the “species” of capture probe refers to their exact position on the substrate (page 20, para. 1), as well as their positional domain (page 31, para. 4). Additionally, Frisén notes that their capture probes need not be on the substrate in a particular orientation, but it is preferred that they have a 3’ end free (pages 7-8 joining para.). Therefore, the capture probes of Frisén may be attached to the substrates at their 5’ ends. In considering the probes of Zhu, for a given position on the solid support of Frisén, capture probes (with the same positional domain/spatial barcode) would be designed, but some of the probes would be for binding to an analyte, while some would be designed for binding to these first capture probes once they have been appropriately extended. Given that this hybridization would only be desired/possible after the first capture probes are extended, the second capture probes would be designed so that they would hybridize to the end sequence of the extended first capture probes – namely, by being at least partially complementary to the complementary sequence to the template switching oligonucleotide on the first capture probes (i.e. at least partially identical to the sequence of the template switching oligonucleotide). As template-switching methodology is well-known (see Frisén page 60, para. 3) and does not rely on an unknown natural sequence, but instead that of an oligonucleotide probe, and Frisén and Zhu both teach methods of probe design (e.g. Frisén page 32, para. 2 and Zhu para. 328), it would be possible to design the second capture probes with this template-switching oligonucleotide sequence in mind. Zhu notes that probe sequences near each other on a solid support may hybridize to one another to form a coupled product that can be used for downstream analysis, providing a reasonable expectation of success that the same could be done with the hybridized capture probes of Frisén.
As noted above, Zhu teaches that their double-stranded probes can be amplified and sequenced. Frisén also teaches amplification and sequencing of extended probe products (for amplification see page 6, para. 3, page 33-34, joining para., page 59, para. 1, page 62, para. 4 and for sequencing see page 19, para. 4, page 43, para. 3, page 48, para. 3, page 59, para. 1, and pages 64-65, joining para.). The ordinary artisan would thus be motivated to make such a combination of Frisén in view of Zhu because when these double-stranded products are analyzed via amplification and sequencing, the second capture probes that were appropriately hybridized to and amplified will be easily identified via sequencing by the number/order of their sequences present on the reads (e.g. the capture probe sequence with the template switching oligonucleotide sequence, the cDNA equivalent of the mRNA sequence, and the complement of the first capture probe sequence). This would indicate probe sequences that successfully went through all of the intended steps of the method, and would allow for the filtering of the sequence reads to only include appropriate sequences in analyses. This would eliminate erroneous reads and/or would indicate if the method was working as intended. Overall, this would increase the accuracy of the method and the confidence in the results.
However, it is noted that in the initial teachings of Frisén, a second cDNA strand is at least partially created. Though it would be prima facie obvious with the teachings of Frisén alone to remove unused/unneeded mRNA and template switching oligonucleotide sequences as described above, this would not necessarily remove the second cDNA strand.
Fu teaches multiplexed amplification methods where amplification and analysis take place on a solid support (Abstract). Throughout the reference, Fu teaches that sequences may be removed via denaturation. Paras. 108-109 and 111 describe removing a target sequence from a probe via denaturation, and these are illustrated in Figures 1B and D and 6B. Figures 1B and D note that after denaturation, additional ligation and transcription can occur utilizing the attached probes. Figure 6B specifically notes that after denaturation, additional sequences may hybridize to the probes on the substrate.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Fu in the method of Frisén in view of Zhu to use denaturation to remove all potential sequences hybridized to the first capture probes so that said probes may undergo additional hybridization/downstream analyses. Generally, Frisén does not specify how sequences may be removed from the probes to make room for further extension/amplification/sequencing reactions, nor does the reference prohibit specific types of removal. The reference does at least hint at denaturation methods, as it teaches qPCR (see page 88, para. 1). Fu specifically teaches using denaturation methods to remove sequences hybridized to probes attached to substrates, as this would not remove the attached probe from said substrate. Thus, the ordinary artisan would recognize that denaturation would be an effective method for the removal of no longer needed sequences that would not affect the attachment of the first and second capture probe sequences in the method of Frisén in view of Zhu. This denaturation method of removal would therefore remove the portion of the second cDNA strand hybridized to the extended first capture probes, and would allow the method of Frisén in view of Zhu to proceed as described above, where the first and second capture probes could hybridize to one another. Using denaturation would simply result in capture probe sequences ready for downstream processes, and as Fu provides evidence that such denaturation methods would be known to the ordinary artisan, there would be a reasonable expectation of success (instant claim 14).
Additionally, as noted above, Frisén teaches that second strand synthesis of the cDNA can occur on the solid support (page 61, para. 1). As the capture probes of Frisén are initially attached to the solid support, when performing additional methods specifically described on the solid support, it would be prima facie obvious to have these capture probes remain attached to said support. Therefore, as the second capture probes of Frisén, in view of Zhu, and in view of Fu are also attached to said solid support, it would also be prima facie obvious to have them remain on the solid support while the two probes hybridize to one another. This would also ensure that the first and second capture probes stay within proximity to one another so that hybridization would be possible.
Thus, by combining Frisén, in view of Zhu, and in view of Fu, this would render obvious steps (a)-(g) of instant claim 2.
Therefore, claims 2 and 14 are prima facie obvious over Frisén, in view of Zhu, and in view of Fu.
Regarding claims 3, 7, and 15, Frisén teaches amplification of probes and double-stranded cDNA products, and Zhu teaches that amplification of the hybridized probes may occur, as described in the rejections above. In the initial creation of the extended first capture probe in the method of Frisén, in view of Zhu, and in view of Fu, dNTPs must be provided in order for the extension to occur. Thus, utilizing dNTPs on the solid support is already established by the combination of references, and is alluded to on page 61, para. 1 of Frisén. Furthermore, in the method of Frisén, in view of Zhu, and in view of Fu, the resulting hybridized first and second capture probes are hybridized in the region containing the template switching oligonucleotide sequence (and the respective complementary sequence). This leaves much of the first capture probe unhybridized, as well as a portion of the second capture probe unhybridized. Before removal from the solid support and downstream amplification/sequencing, it would be prima facie obvious to add additional dNTPs to the solid support to obtain complete hybridization of the capture probes to one another – i.e. extending the 3’ end of the first capture probe to complement the 5’ end of the second capture probe, and fully extending the 3’ end of the second capture probe to complement the middle and 5’ end of the first capture probe. Then, a fully complementary double-stranded probe would be produced, which would be an easier starting product for amplification purposes, as only a single pair of forward and reverse primers would be needed, which would likely not be the case if the probe sequences were not the same length. This would thus simplify (and likely make more accurate) downstream methods. This extension would therefore generate the spatially barcoded extension product as described in the “Claim Interpretation” section above. As noted above, Frisén teaches amplification and sequencing of extended probe products (for amplification see page 6, para. 3, page 33-34, joining para., page 59, para. 1, page 62, para. 4 and for sequencing see page 19, para. 4, page 43, para. 3, page 48, para. 3, page 59, para. 1, and pages 64-65, joining para.) and Zhu teaches that their double-stranded probes can be amplified and sequenced (paras. 354-355 and 386).
Regarding claim 5, Frisén teaches that the capture probes may contain UMI sequences (page 83, para. 9). Though the reference does not specifically state that the second capture probes as described above in the rejection of claim 2 may have UMIs, the ordinary artisan would recognize the utility in providing sequences unique to the second capture probe in the method of Frisén, in view of Zhu, and in view of Fu described above in the rejection of claim 2. Specifically, as this second capture probe is designed to hybridize to (and aid in further amplification/sequencing of) the first capture probe, by including an additional tag in the form of a UMI, this tag would then be incorporated into the extension products. The ordinary artisan would recognize that the second UMI could be used as an additional check during sequence read analysis to ensure that all the intended extension reactions occurred. If the second UMI is not found when sequencing the products, it may indicate an error associated with the method, which would be important to know before interpreting results.
Regarding claim 6, it is first noted that the claim does not state when the 3’ end of the second probe must be blocked in the method of claim 2, or that said second probe must be blocked for the entire method. Frisén teaches that capture probes may be blocked on their 3’ ends prior to contacting the biological specimen (page 51, para. 3) in order to avoid inappropriate or unwanted modification of the capture probes (page 52, para. 1). Frisén also teaches many means by which to block capture probes (page 52, paras. 2-3). Thus, the ordinary artisan would recognize that the second capture probes as described above in the rejection of claim 2 could be similarly blocked before coming into contact with the first capture probes, in order to ensure that no unwanted modification of these probes occurs and that they work as intended. Frisén also teaches means of removing a blocking moiety/domain (page 53, paras. 1 and 3), which would provide a reasonable expectation of success that the second capture probes could be blocked and unblocked as needed to achieve the benefits described by Frisén.
Regarding claim 8, Frisén teaches that the extension of capture probes may be performed with the use of a reverse transcriptase (see page 15-16, joining para. through page 16, para. 2, which references step (c) on pages 5-6).
Regarding claim 9, Frisén teaches that the biological specimen examined may be a tissue section (page 1, para. 3, page 48, para. 3, and page 82, para. 2). Fixed tissues may be used (page 47, para. 2).
Regarding claim 10, Frisén teaches that the biological sample may be permeabilized in order for the nucleic acids within the sample to bind to the capture probes (page 50, paras. 2-4). Applicant does not provide a specific definition for the term “release” in the instant claim, so Frisén’s discussion of permeabilization allowing for interaction of targets with the capture probes is considered to be encompassed by the term.
Regarding claims 11-12, Frisén teaches that the capture probes may be attached to the solid support via a cleavable chemical cross-linker (pages 11-12, joining para.).
Regarding claim 13, Frisén teaches that releasing the capture probes from the surface of the solid support may be done using a cleavage domain such as the cleavable chemical cross-linker (page 11). Frisén also teaches in their examples that cDNA can be released from the array via use of a cleavage mixture incubated with the array at higher temperatures (page 85, para. 4). As Frisén notes that in embodiments in which a second cDNA strand is generated while on the solid support (page 61, para. 1), it would be prima facie obvious that the extended first capture probe would be so extended while still attached to the solid support. Therefore, this cleavage of the capture probes would occur after extension (and therefore, after the generation of the extension product).
Regarding claim 16, Frisén teaches that the amplification/sequencing analysis described above in the rejection of claims 2-3, 7, and 15 may be used to obtain spatial information as to the RNA in the biological specimen (page 6, para. 4). Page 65, para. 3 states, “The sequence of the positional domain (or tag) will identify the feature (or group of adjacent features) from which the capture probe was released and hence the location or vicinity on the solid substrate at which the nucleic acid, e.g. mRNA, molecule was captured. The sequence of the captured nucleic acid, e.g. RNA, molecule may be compared with a sequence database of the organism from which the biological specimen, e.g. tissue sample, originated to determine the gene to which it corresponds. By determining which region (e.g. cell) of the biological specimen, e.g. tissue sample, was in contact with the feature, it is possible to determine which region of the biological specimen, e.g. tissue sample, was expressing said gene (or contained the gene, e.g. in the case of spatial genomics).” This is also taught on page 77, para. 2.
Regarding claim 18, Frisén teaches that the capture probes may also comprise a domain that includes a sequencing primer binding site (page 43, para. 2).
Regarding claim 19, Frisén teaches that the solid substrate of their invention may be a slide (page 22, para. 2 and page 23, para. 2).
Regarding claim 20, this claim differs from instant claim 2 in that the limitations of instant claim 3 are explicitly included in step (h), and step (i) has been added, which involves preparing a sequencing library. Frisén, in view of Zhu, and in view of Fu already render obvious the methods of claims 2 and 3, as described above. Furthermore, Frisén teaches in their working examples the creation of a sequencing library from cDNA sequences (pages 87-88). Thus, in combination with the teachings described above in the rejection of instant claim 2, which teaches the generation of a spatially barcoded extension product, as well as the rejection of instant claim 3, which teaches that a spatially barcoded extension product can be generated by extending the extension product or second probe with the second probe or extension product, respectively, Frisén, in view of Zhu, and in view of Fu also renders obvious the method of claim 20.
Regarding claim 23, the claim requires the same limitations of instant claims 5 and/or 18, with the exception that it depends on instant claim 20, rather than instant claim 2. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2, 5, 18, and 20 as described above, the references therefore also render obvious the method of claim 23.
Regarding claim 24, the claim requires the same limitations of instant claim 7 with the exception that it depends on instant claim 20, rather than instant claims 2-3. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2-3, 7, and 20 as described above, the references therefore also render obvious the method of claim 24.
Regarding claim 25, the claim requires the same limitations of instant claim 15 with the exception that it depends on instant claim 20, rather than instant claims 2-3 and 7. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2-3, 7, 15, and 20 as described above, the references therefore also render obvious the method of claim 25.
Regarding claim 26, the claim requires the same limitations of instant claim 16 with the exception that it depends on instant claim 20, rather than instant claim 2-3, 7, and 15. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2-3, 7, 15-16, and 20 as described above, the references therefore also render obvious the method of claim 26.
Regarding claim 27, the claim requires the same limitations of instant claim 8 with the exception that it depends on instant claim 20, rather than instant claim 2. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2, 8, and 20 as described above, the references therefore also render obvious the method of claim 27.
Regarding claim 28, the claim requires the same limitations of instant claim 9 with the exception that it depends on instant claim 20, rather than instant claim 2. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2, 9, and 20 as described above, the references therefore also render obvious the method of claim 28.
Regarding claim 29, the claim requires the same limitations of instant claim 10 with the exception that it depends on instant claim 20, rather than instant claim 2. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2, 10, and 20 as described above, the references therefore also render obvious the method of claim 29.
Regarding claim 30, the claim requires the same limitations of instant claim 11 (and optionally also instant claim 12) with the exception that it depends on instant claim 20, rather than instant claim 2. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2, 11-12, and 20 as described above, the references therefore also render obvious the method of claim 30.
Regarding claim 31, the claim requires the same limitations of instant claim 19 with the exception that it depends on instant claim 20, rather than instant claim 2. As Frisén, in view of Zhu, and in view of Fu renders obvious the methods of claims 2, 19, and 20 as described above, the references therefore also render obvious the method of claim 31.
Conclusion
No claims are currently 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 FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
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, 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.
/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681