CTNF 18/563,307 CTNF 77336 DETAILED ACTION Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Information Disclosure Statement The IDS received on November 21, 2023 and March 12, 2025 are proper and are being considered by the Examiner. Drawings New corrected drawings in compliance with 37 CFR 1.121(d) are required in this application because a figure showing its multiple views without a corresponding enumeration. 37 CFR 1.84(u)(1) states that, “[t]he different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter .” For example, Figure 2 is comprised of multiple drawing across multiple pages depicting partial aspects, but are all identified as Figure 2. Applicant is advised to employ the services of a competent patent draftsperson outside the Office, as the U.S. Patent and Trademark Office no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance. Claim Objections 07-29-01 AIA Claim s 2 and 3 are objected to because of the following informalities: Claims 2 and 3 recite periods after elements i., ii., iii., and iv. MPEP 608.01(m) clearly states that each claim begins with a capital letter and ends with a period and that, “[p]eriods may not be used elsewhere in the claims except for abbreviations.” Appropriate correction is required. Claim Rejections - 35 USC § 112 07-30-02 AIA The following is a quotation of 35 U.S.C. 112(b): (b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention. The following is a quotation of 35 U.S.C. 112 (pre-AIA), second paragraph: The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention. 07-34-01 Claims 2, 3, 11, and 14-16 are rejected 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 which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claims 2 and 3 are indefinite for reciting the limitation, “the PCR primer amplification sequence” because there are two different instances of a PCR amplification sequence – one of step (a)(ii) and one of step (b)(ii). Referring to the nucleic acids of, for example (b)(ii) does not necessarily require that “the PCR primer amplification sequence” is that of (b)(ii). Claims should be amended to explicitly refer to the PCR primer amplification sequence of the particular step. Claim 11 recites the phrase, “the double-stranded cDNA comprises”. It is unclear whether this phrase is referring to “the double-stranded input cDNA”, or the “first cDNA fragments”, or the “second cDNA fragments”. For the purpose of prosecution, the phrase has been construed to mean, “the double-stranded input cDNA.” Claim 14 recites the limitation, “greater than about.” It is vague and indefinite what is meant by the phrase “greater than about”. The phrase “greater than” typically indicates a starting, minimum point. The phrase “greater than” however, is controverted by the term “about” which implies that values above and below the recited number of nucleotides are permitted. This is analogous to the situation of Amgen, Inc. v. Chugai Pharmaceutical Co., 927 F.2d 1200 (CAFC 1991), wherein the CAFC stated, “The district court held claims 4 and 6 of the patent invalid because their specific activity limitation of ‘at least about 160,000’ was indefinite”. After review, the CAFC states “We therefore affirm the district court's determination on this issue.” Thus, the CAFC found the phrase “at least about” indefinite where the metes and bounds of the term were not defined in the specification. Claims 15 and 16 are indefinite by way of their dependency and using the phrase, “from about”. Claim Rejections - 35 USC § 103 07-20-aia AIA 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. 07-21-aia AIA Claim s 1-9 and 14-18 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 Polymenidou et al. (Nature Neuroscience, February 2011, vol. 14 no. 4, pages 459-468) . With regard to claim 1, 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): PNG media_image1.png 481 438 media_image1.png Greyscale 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). With regard to claim 9, 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 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). 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, 2 nd 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 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. 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 . 07-22-aia AIA Claim s 10-13 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 Polymenidou et al. (Nature Neuroscience, February 2011, vol. 14 no. 4, pages 459-468) , as applied to claim s 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) . Teachings of Gormley et al. and Polymenidou et al. have already been discussed above. Gormley et al. and Polymenidou et al. do not explicitly teach that the double-stranded cDNA comprises a PCR primer amplification sequence at one or both ends (claim 10), or that the double-stranded cDNA comprises a molecular index at one or both ends (claim 12), wherein the molecular index is a diseased cell-type specific barcode (claim 13). Hu et al. teach a method of tagmenting double-stranded cDNA molecule comprising a primer sequence at one or both of its ends, an index at one or both of its ends (UMI, CI) ( see Figure 1, also cell barcode (CI) on page 7), wherein the artisan teach that the method is for determining RNA isomers (“method for sequencing single-cell transcript isomers”, see page 4). 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. and Polymenidou et al. with the teachings of Hu et al., thereby arriving at the invention as claimed for the following reasons. As already discussed above, one of ordinary skill in the art would have been motivated to apply the tagmentation means discussed by Gormley et al. for double-stranded cDNAs produced from various sources 1 . As well, Gormley et al. explicitly teach pooling the tagmented and amplified products for high-throughput sequencing: “once the tagmentation is complete the DNA is transferred from the bead surface to solution so that the individual fragments can be pooled and prepared for sequencing” (section [0121]) In view of the desire to pool the tagmented/amplified products for sequencing, one of ordinary skill in the art would have been motivated to combine the teachings of Hu et al., so as to produce an input cDNA molecule which is comprised of a cell-type indexing sequence before performing the tagmentation step of Gormley et al. so as to compile the sequence of the input cDNA molecules, with information regarding the source ( i.e., cell type) from which the cDNA molecules originated. Therefore, the invention as claimed is deemed prima facie obvious over the cited references. Conclusion No claims are allowed. 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. Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600. 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. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /YOUNG J KIM/Primary Examiner Art Unit 1637 February 24, 2026 /YJK/ Application/Control Number: 18/563,307 Page 2 Art Unit: 1681 Application/Control Number: 18/563,307 Page 3 Art Unit: 1681 Application/Control Number: 18/563,307 Page 4 Art Unit: 1681 Application/Control Number: 18/563,307 Page 5 Art Unit: 1681 Application/Control Number: 18/563,307 Page 6 Art Unit: 1681 Application/Control Number: 18/563,307 Page 7 Art Unit: 1681 Application/Control Number: 18/563,307 Page 8 Art Unit: 1681 Application/Control Number: 18/563,307 Page 9 Art Unit: 1681 Application/Control Number: 18/563,307 Page 10 Art Unit: 1681 Application/Control Number: 18/563,307 Page 11 Art Unit: 1681 Application/Control Number: 18/563,307 Page 12 Art Unit: 1681 Application/Control Number: 18/563,307 Page 13 Art Unit: 1681 1 See Gormley et al., “dsDNA of interest (including double-stranded cDNA prepared from RNA), from any source, for genomic, subgenomic, transcriptomic, or metagenomic analysis, or analysis of RNA expression”, section [0004].