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 .
A preliminary amendment filed August 20, 2024, amending claim 1 and adding new claims 2-28 is acknowledged and has been entered. Claims 1-28 are pending and will be examined.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on September 5, 2023, December 4, 2023, March 5, 2024, June 10, 2024, September 25, 2024, December 19, 2024, March 27, 2025, and June 24, 2025 was filed in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Priority
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 63087061, 62969458 and 62952736 fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. Each of these documents provide insufficient support for the exon specific language within claims 2-3 and 16-17
The earliest priority date with enabling support for claims 2-3 and 16-17 is PCTUS2020066720 with a date of December 22, 2020. The remaining claims 1, 4-15, 18-28 have an earliest priority date of December 23, 2019.
Claim Rejections - 35 USC § 103
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.
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) 1, 4-9, 11, 14-28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (US Patent 10,774,374; September 2020) in view of Van Driel et al. (US PgPub 2018/0112261; April 2018).
With regard to claim 1, Frisen teaches a composition comprising:
(a) a biological sample placed on a first substrate, wherein the biological sample comprises a target nucleic acid;
(b) a second substrate comprising a spatial array comprising a plurality of capture probes affixed to the first substrate, wherein a capture probe of the plurality of capture probes comprises (i) a spatial barcode comprising a sequence that provides a location of the target nucleic acid in the biological sample (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted); and
(c) a ligation product comprising a first probe and a second probe wherein the first probe comprises a first sequence that is substantially complementary to a first target sequence of the target nucleic acid, wherein a second probe comprises (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted; see also col. 5, lines 5-25, where the amplicon can be a ligation product):
(ii) a capture domain, wherein the first substrate is aligned with the second substrate, such that at least a portion of the biological sample is aligned with at least a portion of the spatial array (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 4, Frisen teaches a composition of claim 1, wherein the second probe further comprises a linker sequence between the second sequence and the third sequence, wherein the linker sequence is about 1 nucleotide to about 100 nucleotides in length (col. 24, lines 1-12).
With regard to claim 5, Frisen teaches a composition of claim 4, wherein the linker sequence comprises a barcode sequence that serves as a proxy for identifying the target nucleic acid (col. 24, lines 1-12).
With regard to claim 6, Frisen teaches a composition of claim 1, wherein the first probe and the second probe are substantially complementary to adjacent sequences of the target nucleic acid (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 7, Van Driel teaches a composition of claim 1, wherein the first probe and the second probe hybridize to sequences that are not adjacent to each other on the target nucleic acid (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 8, Frisen teaches a composition of claim 7, further comprising a DNA polymerase (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 11, Frisen teaches a composition of claim 1, wherein the target nucleic acid comprises RNA (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 14, Frisen teaches a composition of claim 1, wherein the biological sample is a formalin-fixed, paraffin-embedded tissue sample, a fresh tissue sample, or a frozen tissue sample (col. 19-20 where the biological sample is a tissue sample or section; see also Example III and IV and where the sample can be formalin-fixed and paraffin embedded or it can be fresh).
With regard to claim 15, Frisen teaches a composition of claim composition comprising:(a) a spatial array comprising a plurality of capture probes affixed to a substrate, wherein a capture probe of the plurality of capture probes comprises (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
(i) a spatial barcode comprising a sequence that provides a location of a target nucleic acid in a biological sample (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted) and
(ii) a capture domain (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted);
With regard to claim 18, Frisen teaches a composition of claim 15, wherein the second probe further comprises a linker sequence between the second sequence and the third sequence, wherein the linker sequence is about 1 nucleotide to about 100 nucleotides in length (col. 24, lines 1-12).
With regard to claim 19, Van Driel teaches a composition of claim 18, wherein the linker sequence comprises a barcode sequence that serves as a proxy for identifying the target nucleic acid (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 22, Frisen teaches a composition of claim 21, further comprising a DNA polymerase (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 25, Frisen teaches a composition of claim 15, wherein the target nucleic acid comprises RNA (col. 2, lines 23-50, where the spatial tagging and the inclusion of primers on the support are described; col. 10, lines 35-52, where the primer or probe sequence is further described; Example III and IV where the spatial localized capture of target mRNA by probes on a solid support is described in more detail; see also Figure 7 and 8, where the process is depicted).
With regard to claim 28, Frisen teaches a composition of claim 15, wherein the biological sample is a formalin-fixed, paraffin-embedded tissue sample, a fresh tissue sample, or a frozen tissue sample (col. 19-20 where the biological sample is a tissue sample or section; see also Example III and IV and where the sample can be formalin-fixed and paraffin embedded or it can be fresh).
Regarding claims 1 and 15, while Frisen teaches a biological sample is applied to a substrate, Frisen does not teach that the tissue is on a different substrate than the substrate with the capture probes, as claimed. Further, while Frisen teaches that the mRNA captured onto the second support can include steps of ligation, Frisen does not exemplify the ligation step.
With regard to claim 1, Van Driel teaches (c) a ligation product comprising a first probe and a second probe wherein the first probe comprises a first sequence that is substantially complementary to a first target sequence of the target nucleic acid, wherein a second probe comprises (Fig 2A-2B, where the probe sequences are depicted which are incorporated into spatial location analysis of analyte and where the ligation process is depicted):
a second sequence that is substantially complementary to a second target sequence of the target nucleic acid; and
a third sequence that is substantially complementary to a third target sequence of the target nucleic acid, and wherein the first probe or the second probe comprises a capture probe capture domain that is complementary to all or a portion of the capture domain of the capture probe affixed to the spatial array (Fig 2A-2B, where the probe sequences are depicted which are incorporated into spatial location analysis of analyte and where the ligation process is depicted and col. 70).
With regard to claim 9, Van Driel teaches a composition of claim 1, wherein the ligation product is hybridized to the capture domain of the capture probe (paragraph 70).
With regard to claim 15, Van Driel teaches (b) the biological sample placed on the spatial array, wherein the biological sample comprises the target nucleic acid (paragraph 9-28, Figure 1, where spatial location of analyte is depicted and described; see also p. 12-14); and
(c) a ligation product comprising a first probe and a second probe, wherein the first probe comprises a first sequence that is substantially complementary to a first target sequence of the target nucleic acid, wherein a second probe comprises: a second sequence that is substantially complementary to a second target sequence of the target nucleic acid; and a third sequence that is substantially complementary to a third target sequence of the target nucleic acid, and wherein the first probe or the second probe comprises a capture probe capture domain that is complementary to all or a portion of the capture domain of the capture probes affixed to the spatial array (Fig 2A-2B, where the probe sequences are depicted which are incorporated into spatial location analysis of analyte and where the ligation process is depicted).
With regard to claim 20, Van Driel teaches a composition of claim 15, wherein the first probe and the second probe are substantially complementary to adjacent sequences of the target nucleic acid (Fig 2A-2B, where the probe sequences are depicted).
With regard to claim 21, Van Driel teaches a composition of claim 15, wherein the first probe and the second probe hybridize to sequences that are not adjacent to each other on the target nucleic acid (Fig 2A-2B, where the probe sequences are depicted).
With regard to claim 23, Frisen teaches a composition of claim 15, wherein the ligation product is hybridized to the capture domain of the capture probe (paragraph 70).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Frisen to include the biological sample or tissue on a first substrate to arrive at the claimed invention with a reasonable expectation for success. Both Frisen and Van Driel teaches many of the features of the composition as claimed, Van Driel teaches tissue attached to a substrate and adding oligonucleotides in solution, while Frisen teaches the oligonucleotide probes are attached to a bead array yet then adds a slice of tissue to the surface of the probes for transfer and hybridization of the mRNA expression molecules. However, it would have been obvious to one of ordinary skill in the art to modify the tissue onto a solid support such as a slide as taught by Van Driel. Regarding this topic, throughout, Van Driel teaches the importance of maintaining the spatial location of tissue and FFPE sample provided on a slide. For example, at protocol C, Van Driel teaches “The tissue sample is deparaffinized, e.g. using deparaffinization solution (e.g. Qiagen) according to the manufacturer's instructions. An image of the complete slide is acquired (Philips Digital Pathology Scanner UFS) and within the image a ROI is identified. Within the ROI different locations are selected and a top selection mask is applied by inkjet printing (print head XAAR) a UV curable ink (Sunjet ink Crystal UFE 7573 (Black)) creating a lattice that separates the different reaction wells. UV curing of the mask is carried out at 360 to 380 nm with a UV-LED for 30 s to 60 s” (paragraph 114-118). It is clear from the teaching that the benefits of the spatial analysis of Van Driel would not be possible without attachment to a slide or other substrate, as claimed. Further, regarding the ligation step, Van Driel teaches “The goal of this experiment was to ligate the miRNA cloning linker on the 3′ side of RNA and to ligate the RNA 5′adapter on the 5′ side of RNA on a FFPET slide in a single reaction” and then the slide was further dried for processing and fixation. Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the teachings of Frisen to include the biological sample or tissue on a first substrate to arrive at the claimed invention with a reasonable expectation for success.
Claim(s) 2-3 and 16-17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (US Patent 10,774,374; September 2020) in view of Van Driel et al. (US PgPub 2018/0112261; April 2018) as applied over 1, 4-9, 11, 14-28 above and further in view of Vickovic et al. (Nature Methods, 2019, vol. 16, p 987-990).
With regard to claim 2, Vickovic teaches a composition of claim 1, wherein the second target sequence and the third target sequence are on different exons of the target nucleic acid (Fig 2, p 989, col. 1, see also “Assessing nuclear RNAs in HDST data” heading, where exons are analyzed against a reference sequence).
With regard to claim 3, Vickovic teaches a composition of claim 1, wherein the second target sequence and the third target sequence are located within the same exon of the target nucleic acid but are not adjacent on the target nucleic acid (Fig 2, p 989, col. 1, see also “Assessing nuclear RNAs in HDST data” heading, where exons are analyzed against a reference sequence).
With regard to claim 16, Vickovic teaches a composition of claim 15, wherein the second target sequence and the third target sequence are on different exons of the target nucleic acid (Fig 2, p 989, col. 1, see also “Assessing nuclear RNAs in HDST data” heading, where exons are analyzed against a reference sequence).
With regard to claim 17, Vickovic teaches a composition of claim 15, wherein the second target sequence and the third target sequence are located within the same exon of the target nucleic acid but are not adjacent on the target nucleic acid (Fig 2, p 989, col. 1, see also “Assessing nuclear RNAs in HDST data” heading, where exons are analyzed against a reference sequence).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Frisen and Van Driel to include the exonic targets as described by Vickovic to arrive at the claimed invention with a reasonable expectation for success. Each of Frisen, Van Driel and Vickovic are focused on spatial expression. Vickovic specifically looks at exonic reads against a reference sequence. In particular, Vickovic teaches “Collecting H&E stains jointly with HDST data allowed us to further relate high-resolution barcodes to sub-cellular features. To demonstrate this, we performed nuclear segmentation and identified transcripts with preferential nuclear localization, by comparing RNAs associated with barcodes within or outside segmented nuclei (Supplementary Fig. 6e,f and Supplementary Table 8). Most of the 186 genes identified as nucleus specific by both HDST and single nucleus RNA-Seq (Methods) were protein coding. Furthermore, HDST barcodes overlapping within segmented nuclei showed significantly higher (P < 0.05, one-sided unpaired Welch’s t-test) ratios of intronic versus exonic reads. This analysis can be extended to other sub-cellular features imaged with dedicated stains (for example, dendrites)” (p. 989, col. 1). Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the teachings of Frisen and Van Driel to include the exonic targets as described by Vickovic to arrive at the claimed invention with a reasonable expectation for success.
Claim(s) 10 and 24 is/are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (US Patent 10,774,374; September 2020) in view of Van Driel et al. (US PgPub 2018/0112261; April 2018) as applied over claims 1, 4-9, 11, 14-28 above and further in view of Fan et al. (US Patent 7361488; April 2008).
With regard to claim 10, Fan teaches a composition of claim 1, wherein the capture domain comprises a poly- thymidine sequence (col. 3-4, where the format of Fan is designed to bind to poly(A) targets; col. 9-10).
With regard to claim 24, Fan teaches a composition of claim 15, wherein the capture domain comprises a poly- thymidine sequence (col. 3-4, where the format of Fan is designed to bind to poly(A) targets; col. 9-10).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Frisen and Van Driel to include the poly-thymidine sequence as taught by Fan to arrive at the claimed invention with a reasonable expectation for success. Regarding the poly(A) or reverse complement, Van Driel teaches “The primer sequence is complementary to the nucleic acids in the sample that are to be targeted. For example, the primer sequence may comprise a poly-T sequence if the total mRNA of the sample is to be targeted or the primer sequence may comprise nucleotides complementary to a sequence stretch of a specific gene if only nucleic acids expressed by said gene are to be targeted” (paragraph 57-58). Further, Fan teaches “Once the hybridization complexes are formed, unhybridized probes are removed. This is important as all target probes may form some unpredictable structure which will complicate the amplification using the universal priming sequences. Thus to ensure specificity (e.g. that target probes directed to target sequences that are not present in the sample are not amplified and detected), it is important to remove all the nonhybridized probes. The separation of unhybridized target probes is done utilizing supports comprising poly(T) sequences” and that “supports (as defined below), particularly magnetic beads, comprising poly(T) sequences are added to the mixture comprising the target sequences and the target probes” (col. 9 of Fan). Therefore, one of ordinary skill in the art at the time the invention was made would have adjusted the teachings of Frisen and Van Driel to include the poly-thymidine sequence as taught by Fan to arrive at the claimed invention with a reasonable expectation for success.
Claim(s) 12 and 26 is/are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (US Patent 10,774,374; September 2020) in view of Van Driel et al. (US PgPub 2018/0112261; April 2018) as applied over claims 1, 4-9, 11, 14-28 above and further in view of Barany et al. (US Patent 9,598,728; March 2017).
With regard to claim 12, Barany teaches a composition of claim 1, further comprising an RNase H enzyme (col. 10, lines 4-9).
With regard to claim 26, Barany teaches a composition of claim 15, further comprising an RNase H enzyme (col. 10, lines 4-9).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Frisen and Van Driel to include the additional features as taught by Barany to arrive at the claimed invention with a reasonable expectation for success. For example, Barany teaches “the present invention is directed to a method for identifying the presence of one or more target nucleotide sequences in a sample. This method involves providing a sample potentially containing the one or more target nucleotide sequences and providing one or more oligonucleotide probe sets”. Further, Barany teaches “The ligated product sequences in the sample are detected and the presence of one or more target nucleotide sequences in the sample is identified based on the detection” (col. 1-2). It is clear from the teaching of Barany and Van Driel that both methods are directed to similar approaches which include ligation steps and array based formats. Therefore, one of ordinary skill in the art at the time the invention was made would adjusted the teachings of Frisen and Van Driel to include the additional features as taught by Barany to arrive at the claimed invention with a reasonable expectation for success.
Claim(s) 13 and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (US Patent 10,774,374; September 2020) in view of Van Driel et al. (US PgPub 2018/0112261; April 2018) as applied over claims 1, 4-9, 11, 14-28 above and further in view of Lao et al. (US Patent 7255994; August 2007).
With regard to claim 13, Lao teaches a composition of claim 1, further comprising proteinase K or pepsin (col. 8, line 51, where proteinase k is used for isolation or purification).
With regard to claim 27, Lao teaches a composition of claim 15, further comprising proteinase K or pepsin (col. 8, line 51, where proteinase k is used for isolation or purification).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Frisen and Van Driel to include the method of extraction as taught by Lao to arrive at the claimed invention with a reasonable expectation for success. Lao teaches “The target nucleic acids for use with the invention may be derived from any organism or other source, including but not limited to prokaryotes, eukaryotes, plants, animals, and viruses, as well as synthetic nucleic acids, for example. The target nucleic acids may originate from any of a wide variety of sample types, such as cell nuclei (e.g., genomic DNA), whole cells, tissue samples, phage, plasmids, mitochondria, and the like. The target nucleic acids may contain DNA, RNA, and/or variants or modifications thereof” (col. 8, lines 39-46). Lao also teaches “Optimally, each of the above purification methods is preceded by an enzyme digestion step to help eliminate protein from the sample, e.g., digestion with proteinase K, or other proteases. Other desirable methods of purification include use of NucPrep™ Chemistry from Applied Biosystems, through the ABI Prism™ 6100 Nucleic Acid PrepStation or the ABI Prism™ 6700 Automated Nucleic Acid Workstation” (col. 8, line 64 to col. 9, line 4). Therefore, one of ordinary skill in the art at the time the invention was made to have adjusted the teachings of Frisen and Van Driel to include the method of extraction as taught by Lao to arrive at the claimed invention with a reasonable expectation for success.
Conclusion
No claims are allowed. All claims stand rejected.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681
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