Prosecution Insights
Last updated: October 04, 2026
Application No. 18/341,436

COMPOSITIONS AND METHODS FOR IDENTIFICATION OF A DUPLICATE SEQUENCING READ

Final Rejection §102§103§112§DP
Filed
Jun 26, 2023
Priority
Nov 13, 2013 — provisional 61/903,826 +4 more
Examiner
PHAM, KHAI QUYNH TIEN
Art Unit
1684
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Tecan Genomics Inc.
OA Round
2 (Final)
0%
Grant Probability
At Risk
3-4
OA Rounds
0m
Est. Remaining
0%
With Interview

Examiner Intelligence

Grants only 0% of cases
0%
Career Allowance Rate
0 granted / 1 resolved
-60.0% vs TC avg
Minimal +0% lift
Without
With
+0.0%
Interview Lift
resolved cases with interview
Typical timeline
3y 3m
Avg Prosecution
44 currently pending
Career history
36
Total Applications
across all art units

Statute-Specific Performance

§101
4.1%
-35.9% vs TC avg
§103
52.1%
+12.1% vs TC avg
§102
15.2%
-24.8% vs TC avg
§112
19.3%
-20.7% vs TC avg
Black line = Tech Center average estimate • Based on career data from 1 resolved cases

Office Action

§102 §103 §112 §DP
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 . Status of the Application Claims 1-7, 13-17, 20, and 22-26 are pending and under examination Claims 1, 7, 13-17, and 20 are amended Claims 22-26 are newly added Claims 8-12, 18-19, and 21 are canceled The following Office Action is in response to Applicant's communication dated 08/03/2026. Any previous rejection(s) and/or objection(s) not repeated in this action are withdrawn. The rejection(s) and/or objection(s) maintained below, along with any newly applied one(s), constitute the complete set presently being applied to the instant application. RE: Applicant argues the amended limitations distinguished the claimed subject matter from previous 35 USC § 102 and 35 USC § 103 rejections over Belias et al. In response: Newly added limitations by Applicant in present amendment, which are considered and will be addressed in present office action. New Claim Rejections - 35 USC § 112(b) Necessitated by amendments 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. Claim(s) 3, 4, and 23 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 3 and 4 recites “the indexing site”, which lacks antecedent basis. The amended claim 1 does not introduce any “indexing site”. Hence the claim is indefinite and the metes and bounds of the claim are unascertainable. Claims 23 recites “each unique identifier”, “the adapter”, and “the nucleic fragment”. Claim 1 instead introduces “identifier site”, “adaptor”, “an amplified original fragment”, “original fragment”, “target nucleic acid sequences”, and “target sequence”. It is unclear whether the newly recited terms refers to previously recited structures, and which fragments form the junction. For purposes of examination only, and to facilitate a complete analysis of the claim, the Examiner interprets the “each unique identifier” as equivalent to “identifier site” of claim 1, “the adapter” as equivalent to “adaptor” of claim 1, and “the nucleic fragment” as equivalent to “original fragment” of claim 1. This interpretation is adopted solely for examination and does not resolve the lack of clarity in the claim language. Modified Claim Rejections - 35 USC § 102 Necessitated by amendments 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention. (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. Claim(s) 1-5, 7, 13-17, 20, 22-26 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bielas et al. (WO2013123442Al, of record). Regarding claim 1, Bielas discloses method for detecting a duplicate sequencing read from a population of sample sequencing reads comprising: obtaining polynucleotides each polynucleotide comprising an amplified original fragment of a nucleic acid with an appended adaptor, wherein each adaptor (e.g. Example 1 and Example 3 involved ligation of a fragment of a nucleic acid into a circular vector, which appended an adaptor made up of AS-Index-PS1-Cypher to the 5ʹ end of the fragment, as shown below in the annotated version of Bielas Figure 2.) adaptor comprises: an identifier site comprising a plurality of nucleotides unique to each original fragment of the nucleic acid (e.g. In both Example 1 and Example 3, Bielas discloses an adaptor with a random Cypher/identifier site to identify duplicate sequencing reads. [pages 26, 28-29] sequencing the polynucleotides thereby generating a population of sequencing reads that include the identifier site nucleotides and target nucleic acid sequences (e.g. In both Example 1 and Example 3, Bielas sequenced the adaptor-ligated fragments on Illumina devices to generate a population of sequencing reads that included the identifier and target sequence. [pages 27, 31] identifying sequencing reads from the population comprising a duplicate identifier site and target sequence. (e.g. Bielas teaches that sequenced fragments can be “computationally deconvoluted” using Cypher fragment sequences to distinguish “true mutations” found in original fragments from “artifact mutations” generated during library preparation. [pages 24-25, 27, 37].) Regarding claim 2, Bielas discloses removing from the population of sequence reads the sequencing read with a duplicate identifier site and target sequence. (e.g. In Example 1 and Example 3, reads with duplicate Cypher-fragment sequences were “deconvoluted” to “original molecules,” i.e., they were de-duplicated, as shown in Figure 3B.). Regarding claim 3, Bielas further discloses the identifier site is sequenced with the indexing site. (e.g. Bielas discloses construct with Cypher/identifier site may further comprise an index sequence so that the library can be pooled with other libraries having different index sequences to facilitate multiplex sequencing. [Fig. 2 and page 20 lines 26-31]) Regarding claim 4, Bielas further discloses identifier site is sequenced separately from the indexing site. (e.g. lllumina devices used by Biel as in Example 1, the indexing site/sample index is read in a separate SBS reaction from the identifier site and the fragment. [page 25 line 51]) Regarding claim 5, Bielas further discloses identifier site is sequenced with the target sequence. (e.g. In both Example 1 and Example 3, Bielas disclosed the use of adaptors in which the Cypher/identifier site and the nucleic acid fragment/target sequence are on the 3ʹ side of the sequencing primer binding site. [pages 24-29]. The POSA would have understood that Bielas therefore sequenced the identifier site with the nucleic acid fragment in at least one read (from PS1 through the Cypher and fragment sequence)) Regarding claim 7, Bielas further discloses each adaptor comprises a primer binding site. (e.g. The adaptors used in Bielas contained multiple primer binding sites. First, the adaptors included the primer binding sites for use in the PCR reaction to copy the adaptor-ligated fragments out of the vector constructs [pages 24-30]. In addition, the adaptors used in Example 1 and Example 3 include two standard Illumina primer binding sites: a primer binding site to read the sample index and a primer binding site to read the nucleic acid fragment and identifier site. [pages 24-30]) Regarding claims 13 and 14, Bielas further discloses the nucleic acid fragments are cDNA, DNA fragments, RNA fragments, or DNA/RNA fragments. [page 5 line 31, page 9 lines 1-20, page 12, lines 6-10, page 13 lines 17-25] Regarding claim 15, Bielas further discloses each adaptor comprises an indexing site. (e.g. In both Example 1 and Example 3, Bielas disclosed the use of an adaptor that includes a sample index. [pages 24-31]) Regarding claims 16 and 17, Bielas further discloses each unique identifier site sequences at least 6 nucleotides in length. (e.g. Bielas teaches several values for the cypher length, including ranges of 7-9 [page 20], and specific values of six, seven, or eight nucleotides [page 15]. In Example 3, Bielas used a 7 nucleotide identifier [pages 24-29].) Regarding claim 20, Bielas further discloses the primer binding site is a universal target sequence primer binding site. (e.g. In Examples 1 and 3, Bielas’s adaptors included a standard Illumina sequencing/target sequence primer binding site that is the same in all of the adaptors, and thus a “universal target sequencing primer binding site.” [pages 24-30]) Regarding claim 22, Bielas further discloses the adaptors have been appended to the fragments using a ligation reaction or a priming reaction. (e.g. In both Examples 1 and 3, Bielas ligated the adaptors to the fragments. [pages 24-29]) Regarding claim 23, Bielas further discloses unique identifier is at a junction between the adapter and the nucleic fragment. (e.g. Cypher/ identifier locates between adapter and target DNA fragments [Fig. 2]) Regarding claim 24, Bielas further discloses determining the genomic start position for each sequencing read. (e.g. In Example 1, Bielas explains that sequencing reads were “computationally deconvolute[d]” using the Cypher and the position of the fragment mapped against the reference genome [pages 25-27]. In Example 3, Bielas explains that “[s]equences were then compared to wild-type TP53 sequence.” [page 4]. When comparing the fragment sequence to known human genes in Example 1 and Example 3, Bielas determined the genomic start position.) Regarding claim 25, Bielas further discloses obtaining a sample comprising the nucleic acid, fragmenting the nucleic acid to yield the original fragments of the nucleic acid, appending the adaptors to the original fragments of the nucleic acid, and performing an amplification reaction to obtain the polynucleotides. (e.g. In Example 1, Bielas obtained samples of genomic DNA, fragmented the DNA, ligated the fragments to adaptor containing vectors, and then amplified the adaptor-ligated fragments. [pages 24-25]) Regarding claim 26, Bielas further discloses the polynucleotides include an amplified original fragment of a nucleic acid from a first sample with an appended adaptor that includes a first index and an amplified original fragment of a nucleic acid from a second sample with an appended adaptor that includes a second index, and the method includes separating sequence reads by sample based on the first or second index. (e.g. Bielas discloses the use of a sample index in an adaptor in Example 1 and Example 3, including a standard Illumina sample index sequence in Example 3 [pages 24-29]. The purposes of these sample indexes was to pool multiple samples for multiplexed sequencing [page 20 lines 26-31]) Modified Claim Rejections - 35 USC § 103 Necessitated by amendments 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. 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) 6, 24-26 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bielas et al. (WO2013123442Al, of record). Regarding claim 6, Bielas discloses the use of Illumina devices to sequence the adaptor-nucleic acid fragments in Example 1 and Example 3. [pages 24-31]. Bielas further disclosed the use of adapters appended to either end of the nucleic-acid fragment [pages 28-29]; The POSA would have known that the use of adaptors on either end of the fragment allowed for paired-end sequencing on the Illumina devices. In paired end sequencing, the Illumina device would first read one adaptor through the identifier and into the fragment sequence. Then, in the second read, the device would read the fragment from the other direction through the second adaptor sequence on the other end of the fragment, but not the first identifier site that was sequenced in the first read [pages 28-29, Fig. 3B]. Accordingly, in paired end reads, the POSA would recognize that some identifier sites were read separately from the fragment read on the paired-end strand. Given the known benefits of paired-end sequencing, including maximizing the length of the fragment read, the POSA would have been motivated to use paired-end sequencing in the methods disclosed by Bielas, and would have had a reasonable expectation of success in doing so. Furthermore, the choice of sequencing the identifier with the fragment sequence or separately via paired-end sequencing or otherwise was the type of routine design choice that the POSA routinely encountered in NGS experimental design. See Uber Tech., 957 F.3d at 1340. The POSA would have recognized that there were only two choices—sequence the identifiers “with” the fragment sequence or “separately.” The claimed limitation does not disclose any unexpected properties of sequencing the identifiers “separately” from the fragment sequences. Regarding claim 24, to the extent claim 24 is not anticipated by Bielas, it is obvious over Bielas. As explained, Bielas taught that sequencing reads generated in Example 1 and Example 3 were aligned with a reference genome. The POSA would have known that the genomic start position could be determined by aligning a sequencing to a reference genome. The POSA would have recognized that sequence alignment was a standard part of NGS data processing with obvious benefits, including to detect mutations from the reference genome. Thus, based on Bielas, the POSA would have been motivated to practice the method of claim 12 and would have had a reasonable expectation of success in doing so. Regarding claim 25, to the extent claim 25 is not anticipated by Bielas, it is obvious over Bielas. Bielas taught each of the limitations of this claim in Example 1. Bielas further taught library preparation methods that include each of these limitations and specifically explained that libraries of nucleic acids for use in the method could be generated by fragmentation using several techniques [page 9]. Thus, based on Bielas’s teachings, the POSA would have been motivated to practice the method of claim 15 and would have had a reasonable expectation of success in doing so. Regarding claim 26, to the extent claim 26 is not anticipated by Bielas, it is obvious over Bielas. In both Example 1 and Example 3, Bielas discloses the use of a sample index standard for use on Illumina devices. Bielas further discloses that the method is suitable for sample multiplexing, which Bielas explains involves using a unique sample index for each sample and then separating reads based on the unique index [page 20 lines 26-31]. The POSA further would have understood that pooling samples with unique sample indexes prior to sequencing on an Illumina device was a routine technique used in NGS to save costs and time, and would have resulted in sequencing data separated by sample index, i.e. separated by sample. Thus, based on Bielas’s teachings, the POSA would have been motivated to practice the method of claim 16 and would have had a reasonable expectation of success in doing so. Modified Double Patenting Necessitated by amendments The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969). A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b). The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13. The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer. U.5.11,098,357 B2 Claim(s) 1, 2, 5-7, 13-17, 20, 22, and 23 rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1-10 of U.S. Patent No. 11098357 B2 (the '357 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent. Regarding present claims 1, the claim of the '357 patent discloses method for detecting a duplicate sequencing read from a population of sample sequencing reads comprising: obtaining polynucleotides each polynucleotide comprising an amplified original fragment of a nucleic acid with an appended adaptor, wherein each adaptor comprises: an identifier site comprising a plurality of nucleotides unique to each original fragment of the nucleic acid; and sequencing the polynucleotides thereby generating a population of sequencing reads that include the identifier site nucleotides and target nucleic acid sequences; and identifying sequencing reads from the population comprising a duplicate identifier site and target sequence. (e.g. as per claim 1 of the '357 patent) Regarding present claim 2, the claim of the '357 patent discloses removing from the population of sequence reads the sequencing read with a duplicate identifier site and target sequence. (e.g. as per claim 2 of the '357 patent) Regarding present claim 5, the claim of the '357 patent discloses the identifier site is sequenced with the target sequence. (e.g. as per claim 3 of the '357 patent) Regarding present claim 6, the claim of the '357 patent discloses the identifier site is sequenced separately from the target sequence. (e.g. as per claim 4 of the '357 patent) Regarding present claim 7, the claim of the '357 patent discloses each adaptor comprises a primer binding site. (e.g. as per claim 1 of the '357 patent) Regarding present claim 13, the claim of the '357 patent discloses the nucleic acid fragments are DNA fragments, RNA fragments, or DNA/RNA fragments. (e.g. as per claim 5 and 6 of the '357 patent) Regarding present claim 14, the claim of the '357 patent discloses polynucleotides comprise amplified fragments of cDNA. (e.g. as per claim 5 and 6 of the '357 patent) Regarding present claim 15, the claim of the '357 patent discloses each adaptor comprises an indexing site. (e.g. as per claim 1 of the '357 patent) Regarding present claim 16, the claim of the '357 patent discloses each unique identifier site sequences at least 6 nucleotides in length. (e.g. as per claim 8 of the '357 patent) Regarding present claim 17, the claim of the '357 patent discloses the identifier site is between 1 and 10 nucleotides in length. (e.g. as per claim 1 of the '357 patent) Regarding present claim 20, the claim of the '357 patent discloses the primer binding site is a universal target sequence primer binding site. (e.g. as per claim 7 of the '357 patent) Regarding present claim 22, the claim of the '357 patent discloses the adaptors have been appended to the fragments using a ligation reaction or a priming reaction. (e.g. as per claim 1 of the '357 patent) Regarding present claim 23, the claim of the '357 patent discloses each unique identifier is at a junction between the adapter and the nucleic fragment. (e.g. as per claim 10 of the '357 patent) U.S. 11,725,241 B2 Claim(s) 1, 2, 5-7, 14-16, 20, and 22-26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1-16 of U.S. Patent No. 11725241 B2 (the '241 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent. Regarding present claims 1, the claim of the '241 patent discloses method for detecting a duplicate sequencing read from a population of sample sequencing reads comprising: obtaining polynucleotides each polynucleotide comprising an amplified original fragment of a nucleic acid with an appended adaptor, wherein each adaptor comprises: an identifier site comprising a plurality of nucleotides unique to each original fragment of the nucleic acid; and sequencing the polynucleotides thereby generating a population of sequencing reads that include the identifier site nucleotides and target nucleic acid sequences; and identifying sequencing reads from the population comprising a duplicate identifier site and target sequence. (e.g. as per claim 1 of the '241 patent) Regarding present claims 2, the claim of the '241 patent discloses the method further comprises removing from the population of sequence reads the sequencing read with a duplicate identifier site and target sequence. (e.g. as per claim 2 of the '241 patent) Regarding present claims 5, the claim of the '241 patent discloses the identifier site is sequenced with the target sequence. (e.g. as per claim 3 of the '241 patent) Regarding present claims 6, the claim of the '241 patent discloses the identifier site is sequenced separately from the target sequence. (e.g. as per claim 4 of the '241 patent) Regarding present claims 7, the claim of the '241 patent discloses each adaptor comprises a primer binding site. (e.g. as per claim 7 of the '241 patent) Regarding present claims 14, the claim of the '241 patent discloses the polynucleotides comprise amplified fragments of cDNA. (e.g. as per claim 5 of the '241 patent) Regarding present claims 15, the claim of the '241 patent discloses each adaptor further comprises an indexing site. (e.g. as per claim 13 of the '241 patent) Regarding present claims 16, the claim of the '241 patent discloses each unique identifier site sequences at least 6 nucleotides in length. (e.g. as per claim 9 of the '241 patent) Regarding present claims 20, the claim of the '241 patent discloses the primer binding site is a universal target sequence primer binding site. (e.g. as per claim 8 of the '241 patent) Regarding present claims 22, the claim of the '241 patent discloses the adaptors have been appended to the fragments using a ligation reaction or a priming reaction. (e.g. as per claim 10 of the '241 patent) Regarding present claims 23, the claim of the '241 patent discloses each unique identifier is at a junction between the adapter and the nucleic fragment. (e.g. as per claim 11 of the '241 patent) Regarding present claims 24, the claim of the '241 patent discloses determining the genomic start position for each sequencing read. (e.g. as per claim 12 of the '241 patent) Regarding present claims 25, the claim of the '241 patent discloses obtaining a sample comprising the nucleic acid, fragmenting the nucleic acid to yield the original fragments of the nucleic acid, appending the adaptors to the original fragments of the nucleic acid, and performing an amplification reaction to obtain the polynucleotides. (e.g. as per claim 15 of the '241 patent) Regarding present claims 26, the claim of the '241 patent discloses the polynucleotides include an amplified original fragment of a nucleic acid from a first sample with an appended adaptor that includes a first index and an amplified original fragment of a nucleic acid from a second sample with an appended adaptor that includes a second index, and the method includes separating sequence reads by sample based on the first or second index. (e.g. as per claim 16 of the '241 patent) 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. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET. 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, Heather Calamita can be reached at (571) 272-2876. 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. /KHAI QUYNH TIEN PHAM/Examiner, Art Unit 1684 /JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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Prosecution Timeline

Jun 26, 2023
Application Filed
Apr 01, 2026
Non-Final Rejection mailed — §102, §103, §112
Aug 03, 2026
Response Filed
Sep 15, 2026
Final Rejection mailed — §102, §103, §112 (current)

Precedent Cases

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Pri-mirna libraries and methods for making and using pri-mirna libraries
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Prosecution Projections

3-4
Expected OA Rounds
0%
Grant Probability
0%
With Interview (+0.0%)
3y 3m (~0m remaining)
Median Time to Grant
Moderate
PTA Risk
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