DETAILED ACTION
The present Office Action is responsive to the Amendment received on October 4, 2026.
Preliminary Remark
Claims 9-12 are canceled.
Drawings
The corrected drawings received on June 23, 2026 are acceptable.
Claim Objections
The objection made to claims 2 and 3 for containing a period within the claim, as discussed in the Office Action mailed on February 26, 2026 is withdrawn in view of the Amendment received on June 23, 2026.
Claim Rejections - 35 USC § 112
The rejection of claims 2, 3, 11, and 14-16 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter, made in the Office Action mailed on February 26, 2026 is withdrawn in view of the Amendment received on June 23, 2026.
Claim Rejections - 35 USC § 103
The rejection of claims 1-9 and 14-18 under 35 U.S.C. 103 as being unpatentable over Gormley et al. (US 2014/0194324 A1, published July 10, 2014) in view of Polymenidou et al. (Nature Neuroscience, February 2011, vol. 14 no. 4, pages 459-468), made in the Office Action mailed on February 26, 2026 is withdrawn in view of the Amendment received on June 23, 2026.
The rejection of claims 10-13 under 35 U.S.C. 103 as being unpatentable over Gormley et al. (US 2014/0194324 A1, published July 10, 2014) in view of Polymenidou et al. (Nature Neuroscience, February 2011, vol. 14 no. 4, pages 459-468), as applied to claims 1-9 and 14-18 above, and further in view of Hu et al. (CN110643692, published January 3, 2020, IDS reference, using Google machine translation, attached herein), made in the Office Action mailed on February 26, 2026 is withdrawn in view of the Amendment received on June 23, 2026.
Rejection – New Grounds, Necessitated by Amendment
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.
Claims 1-9 and 13-18 are rejected under 35 U.S.C. 103 as being unpatentable over Gormley et al. (US 2014/0194324 A1, published July 10, 2014) in view of Lafzi et al. (Nature Protocols, December 2018, pages 2742-2757) and Polymenidou et al. (Nature Neuroscience, February 2011, vol. 14 no. 4, pages 459-468).
With regard to claims 1 and 13, Gormley et al. teach a method of fragmenting double-stranded cDNA on a support (“methods and composition especially relate to … fragmenting and tagging DNA using transposon compositions immobilized to a solid support … any dsDNA of interest (including double-stranded cDNA prepared from mRNA), from any source for genomic, subgenomic, transcriptomic, or metagenomic analysis, or analysis of RNA expression”, section [0004]), comprising:
contacting double-stranded input cDNA with a plurality of transposomes that are tethered to a support, wherein the tethered transposomes comprise:
a transposase; and
a nucleic acid that is tether to the support and comprises a support barcode and a PCR primer amplification sequence (“providing a solid support having transposome complexes immobilized thereon, wherein the transposome complexes comprise a transposase bound to a first polynucleotide, the first polynucleotide comprising (i) a 3’ portion comprising a transposon end sequence, and (ii) a first tag comprising a first tag domain”, section [0005]; also see Fig. 13, wherein the immobilized transposome complex comprises a transposase, a nucleic acid comprising a primer region and a barcode region); wherein the contacting step (a) results in tagmentation of the cDNA to produce first cDNA fragments that are tethered to the support (see Fig. 14, for example, wherein the double-stranded nucleic acid molecule are immobilized as fragments to the support); and
contacting the product of (a) with a plurality of untethered transposomes, wherein the untethered transposomes comprise:
a transposase; and
a nucleic acid that comprise a PCR primer amplification sequence (“method can further comprise (c) providing transposome complexes in solution and contacting the transposome complexes with the immobilized fragments under conditions, whereby the target DNA is fragmented by the transposome complexes in solution; thereby obtaining immobilized nucleic acid fragments having one end in solution … the transposome complexes in solution can comprise a second tag, such that the method generates immobilized nucleic acid fragments having a second tag, the second tag in solution. The first and second tags can be different or the same”, section [0005]); wherein the contacting step (b) results in tagmentation of at least some of the first cDNA fragments of (a) to produce second cDNA fragments that have: i) the support barcode and ii) a PCR primer amplification sequence at both ends (the result of the step [0005] would result in this structure, see Fig. 4a, for general structure produced).
With regard to claim 2, the nucleic acids of (a)(ii) produced from the tethered complex shown from the below reproduced structure (from Fig. 13):
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As seen, the structure comprises: i) transposon ends that are bound to the transposase (the square blocks); ii) the barcode; iii) the PCR primer amplification sequence; and iv) an end that is tethered to the support), and this being ligated to the double-stranded nucleic acid of the above depicted steps would result in the structure of nucleic acid of (a)(ii) (see Fig. 4a for general structure produced).
With regard to claim 3, the free ends (i.e., untethered end) would be the same as discussed above where in the solution transposome complex comprises a second tag sequence that is the same as the first tag sequence, see section [0005]).
With regard to claim 4, the first and second fragments are amplified (see Fig. 4b).
With regard to claim 5, the amplified fragments are sequence (“determining the sequence of said first and second portions of the target DNA”, section [0011]).
With regard to claim 6, the artisans explicitly teach that the sequence is assembled based on the barcodes that contain (“[b]arcode-assisted assembly of DNA fragments enables isolation of individual long DNA molecules … and conversion of each molecule into a uniquely barcoded sub-fragment library. When the entire population of sub-fragmented DNA molecules is sequenced, the subfragments can be assembled back into there original long molecule by reference to the barcodes they contain”, section [0110]).
With regard to claim 7, the artisans teach the use of unique barcodes for each DNA molecule (i.e., same barcode for the same DNA molecule, but different among different DNA molecule, see “aliquoting into separate compartments (e.g., wells of plate), such that each well contains only one or just few molecules of DNA. Because each well is physically separate, a library preparation can be done in each well with a unique barcode. Thereafter the contents of the wells are pooled and sequenced”, section [0111]).
With regard to claim 8, the support is a bead (see above).
The support barcode is bead-specific (since unique barcode embodiment discussed above, is specific to that bead being employed).
With regard to claims 14-16, the second double-stranded nucleic acid fragment is no more than 700 nucleotides (“the transposom complexes will added DNA, thus generating ds fragments coupled at both ends to the surface … length of the resulting bridged fragments is less than 100 bp, 200 bp, … 700 bp…”, section [0059]; also starting nucleic acid molecule is greater than about 500 bases, “the long strand of target DNA can be at least 0.1kb, 1kb, …20 kb”, section [0074]).
While Gormley et al. explicitly teach that their method is applicable to any double-stranded DNA as well as double-stranded cDNA, the artisans do not provide specific teachings related to using double-stranded cDNA molecules in their tagmentation method.
Consequently, Gormley et al. do not explicitly teach the input cDNA comprises
A cell type-specific barcode (at one or both ends), a UMI, and a TSO sequence (claim 1, in-part), or a nucleotide sequence that is complementary to a target RNA isoform (claim 17), said isoform being indicative of a disease state of a cell (claim 18), wherein the cell type-specific barcode is a diseased cell type-specific barcode (claim 13).
Lafzi et al. teach a method of single-cell RNA sequencing, wherein the artisans teach the production of cDNA with cell-specific barcode, UMI (see Figure 1, Single-cell RNA sequencing). Lafzi et al. also a well-known means of attaching rGrGrG at the 3’ end of the cDNA end after RT (see Table 1), which is typically utilized to append desired indexing additional sequences (“a template-switching oligonucleotide (TSO) binds to the extra cytosine and provides the template for the addition of PCR adaptor sequences for subsequent cDNA amplification”, page 2748)1.
Lazi et al. also teach the profiling of blood cell subtypes, such as cancer (page 2746, 1st column).
Polymenidou et al. teach a well-known means of sequencing RNA isoforms related to disease state (“common approach for identifying specific RNA-binding protein targets or aberrantly spliced isoforms related to disease …”, page 459, 2nd column).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Gormley et al. with the teachings of Lafzi et al. and Polymenidou et al., thereby arriving at the invention as claimed for the following reasons.
As discussed above, Gormley et al. teach a method of tagmenting double-stranded nucleic acid onto a solid substrate comprising all of the claimed steps with an explicit suggestion that the method can be applied to double-stranded cDNA molecules.
“methods and composition especially relate to … fragmenting and tagging DNA using transposon compositions immobilized to a solid support … any dsDNA of interest (including double-stranded cDNA prepared from mRNA), from any source for genomic, subgenomic, transcriptomic, or metagenomic analysis, or analysis of RNA expression” (Gormley et al., section [0004])
Given such a suggestion, one of ordinary skill in the art would have been motivated, as well as would have expected that applying the method of Gormley et al. and using double-stranded cDNAs as the input starting double-stranded DNAs would have yielded the same predictable outcome as since both starting materials would have comprised the same A, G, T, and C bases in a doubles-stranded form, expected to react the same way.
In addition, one of ordinary skill in the art would have been well-motivated to utilize cDNA molecules which have been prior labeled with their cell-specific barcode and UMI for the obvious benefit of analyzing single-cell contents, such as cancer cells, wherein the cell-specific barcode in combination with UMI would have provided the source of the sequence reads from high-throughput sequencing reactions, similar to that employed by Gormley et al. Since attachment of such sequences utilizing a TSO sequence had been well-established and common, such a cDNA molecule would have had a TSO sequence at one of its end.
As well, applying sequencing reaction to RNA molecules, such as isoforms associated with disease state of a cell would have been an obvious application as doing so have been well-established in the art, as evidenced by Polymenidou et al. above and also conceded by Applicants’ own admission:
“differential RNA isoform usage has been shown to be essential in delineating cellular identify and function, and has been demonstrated as an accurate biomarker in a wide range of diseases … method of the present disclosure is used to detect differential RNA isoform usage and/or missplicing, e.g., in diseased vs. non-diseased states, in development and in other cellular processes, See, e.g., Polymenidou et al. (2011) Nat. Neurosci., 14:459 …” (sections [0051]-[0052])
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
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.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 September 11, 2026
/YJK/
1 See WO 2015/168161, Fig. 2A evidences such well-known means.
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