DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 46-65 are pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 12/15/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner, except where noted.
The information disclosure statement filed 12/15/2026 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. Specifically, a copy of the non-patent literature reference Tian et al. has not been provided, and so this reference has not been considered. Applicant has noted that this reference has been submitted in their Remarks (see page 10), but it does not appear in the file wrapper.
Response to Applicant’s Amendments
Priority
Applicant has amended independent claim 46 to remove previous option (d)(i). This option did not have support in the prior filed application, 63/291,146. Thus, the claims are now given the priority date of 12/17/2021 based on the effective filing date of the prior-filed application.
Drawing Objections
The drawings were objected to for including reference characters not mentioned in the description and because Figures 2C-5B were not legible. In light of Applicant’s amendments to the drawings and the specification submitted 12/15/2025, these objections have been withdrawn.
Claim Objections
Claims 47, 51, 55-58, and 62-65 were objected to due to minor informalities. In light of Applicant’s amendments to the claims submitted 12/15/2025, these objections have been withdrawn.
35 USC 112(a) Rejections
Claims 46-65 were rejected for new matter associated with claim 46. In light of Applicant’s amendments to the claims submitted 12/15/2025, these rejections have been withdrawn.
35 USC 112(b) Rejections
Claims 51-53 were rejected for indefiniteness issues associated with claim 51. In light of Applicant’s amendments to the claims submitted 12/15/2025, these rejections have been withdrawn.
35 USC 103 Rejections
Claims 46-65 were rejected as being unpatentable over Evans et al. (US 2017/0355984 A1) in view of Peng et al. (Nature Scientific Reports, 2019), and various combinations of references. In light of Applicant’s amendments to the claims submitted 12/15/2025, these rejections have been withdrawn, but see new grounds of rejection below.
Nonstatutory Double Patenting Rejections
Claims 46-50 and 59 were provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 8-10 of copending Application No. 18/980,172 in view of Peng et al. (Nature Scientific Reports, 2019).
Claims 46-58 and 60 were provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16, 18-23, 27, and 29-35 of copending Application No. 18/980,172 in view of Evans et al. (US 2017/0355984 A1) and Peng et al. (Nature Scientific Reports, 2019).
As Applicant points out in their Remarks (pages 14-15), the claims of the ‘172 application utilized in the above nonstatutory double patenting rejections have been previously canceled. Therefore, these rejections have been withdrawn.
Response to Applicant’s Arguments
Regarding the 35 USC 103 Rejections cited in the Non-Final Rejection mailed 8/14/2025, Applicant argues that the cited references do not disclose steps (d) and (e) of newly amended claim 46. Particularly, Applicant uses the teachings of the specification to support that neither Evans nor Peng teach trimming (or “skipping”) of bases between the UMI and the sample nucleic acid sequence as claimed (Remarks, pages 13-14).
Firstly, as recited in the “Claim Interpretation” section of the Non-Final Rejection, the word “trimming” is not defined by the instant specification. Applicant points out a particular example from the instant specification (see para. 255) where the word “trimmed” was used, but this is not a limiting definition of the term. The term is also not used elsewhere in the specification. MPEP 2111 I states, “Under a broadest reasonable interpretation (BRI), words of the claim must be given their plain meaning, unless such meaning is inconsistent with the specification. The plain meaning of a term means the ordinary and customary meaning given to the term by those of ordinary skill in the art at the relevant time…The presumption that a term is given its ordinary and customary meaning may be rebutted by the applicant by clearly setting forth a different definition of the term in the specification. In re Morris, 127 F.3d 1048, 1054, 44 USPQ2d 1023, 1028 (Fed. Cir. 1997) (the USPTO looks to the ordinary use of the claim terms taking into account definitions or other "enlightenment" contained in the written description); But c.f. In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1369, 70 USPQ2d 1827, 1834 (Fed. Cir. 2004) ("We have cautioned against reading limitations into a claim from the preferred embodiment described in the specification, even if it is the only embodiment described, absent clear disclaimer in the specification.").” Additionally, MPEP 2111 II states, “"Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment." Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).”
In considering this guidance in view of the instant claims, the specification does not provide a limiting definition of the term “trimming.” The embodiment shown in the working example may mean that the trimmed bases are “skipped” in sequence reads, as Applicant notes in their Remarks, but this singular example cannot be said to read on the entirety of the broadest reasonable interpretation of the term in the claims. Thus, the broadest reasonable interpretation of the term must be given its plain meaning in view of the specification and prior art. This broadest reasonable interpretation of trimming also includes removal of the sequence that is trimmed. This is also supported by the claim language itself, where step (d) of claim 46 states that the trimming comprises “removal of one or more bases.”
In light of this interpretation in the context of the claimed method, step (d) states that the trimming comprises removing a sequence between the unique molecular identifier and the sample nucleic acid sequence. Since the trimming comprises this removal, it can also include the removal of additional bases. See MPEP 2111.03 I, which states that the use of comprising “is inclusive or open-ended and does not exclude additional, unrecited elements or method steps.” Thus, as long as the prior art teaches the removal of a sequence between the UMI and the sample nucleic acid sequence, it will read on the instant claim, even if it teaches the removal of other sequences, such as the entirety of the polynucleotide adapters or the UMIs.
In the rejection of Evans in view of Peng presented in the Non-Final Rejection, the adapters of Evans are used with the sequencing analysis of Peng. In the cited teachings of Evans, the UMIs are adjacently attached to the sample sequence. Thus, if they were trimmed as described by the teachings of Peng, there would be no sequence between the UMI and sample that would also be trimmed. Thus, these specific teachings do not read on the newly amended claim 46.
However, there are teachings of these references that are relevant to the newly amended claim. Evans for instance teaches overhangs on their adapter sequences that would be between a UMI and a target sequence (e.g. paras. 22, 52, and Figure 2). In Peng, single-end duplex-UMI adapters are used. These adapters are shown in Figure 1b, and are also noted to contain labels (the red “TT” and “GG” sequences, see page 3, para. 2). Note that the adapters have the UMIs in the middle of the reads, and the label on the top strand of the adapter is closer to the target sequence (Figures 1b-c). These adapters are used during amplification (Figure 1c). On page 8, para. 3 of the reference, during sequence read processing, it is stated that all exogenous sequences, including the UMIs and labels, were removed from the reads. This process involves trimming the reads, as evidenced by the use of the phrase “trimmed reads” in line 3 of the paragraph. Thus, because of the structure of the adapters of Peng, this trimming removes both sequences between the UMI and the sample sequence (e.g. the portion of the top strand adapter between the UMI and the sample), as well as the UMI, and the adapter sequence in general. As described above, such removal reads on step (d) of the claim. The UMIs and labels of Peng were then used as tags for sequencing reads to identify errors. Variants that were not amplification/sequencing errors would then be SNVs, which Peng states they are able to accurately detect (Abstract and Figures 3-4, for example).
As claim 46 comprises the listed steps, and the claim does not specify what may constitute “organizing the plurality of reads based on the plurality of unique molecular identifiers,” in step (e), the appending the UMIs and labels and utilizing them as tags as described in Peng is considered to read on this limitation.
Thus, while Applicant’s amendments to claim 46 have obviated the previous obviousness rejections, Evans in view of Peng still provide teachings relevant to the instant invention, and are utilized in the new grounds of rejection below.
Claim Interpretation
In instant claim 46, the phrase “trimming” is not defined by the instant specification. The claim itself requires removal of bases from each of the sequence reads, where this removal must at least occur between the UMI and the sample sequence. Additional bases can be removed, as evidenced by the use of the “comprises removal” language in the claim. Thus, prior art which comprises the removal of the claimed sequence, as well as the entirety of a UMI and/or the entirety of an adapter, will thus be considered to meet this limitation. Figure 19B supports this interpretation, as it refers to UMI and adapter trimmed reads.
In instant claim 51, the phrase “terminal adapter region” is not defined by the instant specification. Thus, any region at the end of an adapter can be considered terminal, and therefore this region is considered inherent to the structure of an adapter.
In instant claim 61, step (iii) is not specific about how the merging of tagged unaligned and aligned reads should occur. In the instant specification, this appears to simply involve utilizing the UMI tags originally associated with the unaligned sequence reads with the aligned sequence reads before the consensus sequences are created (page 85, para. 2). Thus, any prior art which utilizes UMI tags and aligned sequence reads in the formation of a consensus sequence will be considered to meet this limitation.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 46-54 and 59-61 are rejected under 35 U.S.C. 103 as being unpatentable over Evans et al. (US 2017/0355984 A1) in view of Peng et al. (Nature Scientific Reports, 2019).
Evans teaches methods of sequencing related to genetic variants using sequencing adaptors, with the goal of identifying sequencing errors (Abstract). The sample nucleic acid can be genomic DNA (paras. 187, 657, 661, and 666; instant claim 60). The sequencing method involves sequencing amplified first and second strands of a duplex nucleic acid molecule, where said molecule is ligated to a sequencing adapter prior to being amplified (paras. 9 and 20). The sequencing adapter is double-stranded, where each strand contains a molecular barcode region that is complementary to the corresponding region on the second strand (para. 138 and Figure 1A, characters 10 and 10’). Evans notes that the molecular barcode can be a unique molecular identifier (para. 5; instant claims 47 and 54). The sequencing adapter additionally comprises a duplex region on each strand, where the duplex regions are complementary to one another (para. 138 and Figure 1A, characters 20 and 20’). These would correspond to the yoke regions of the instant claims. Non-complementary regions (reference characters 30 and 30’) are also included on the adapters (instant claim 52). As noted above, terminal adapter regions are considered inherent to the structure of an adapter, and so would be included at each end of the sequencing adapter (instant claim 51). The number of unique molecular identifiers used can be at least 8 and not more than 48 (para. 140; instant claims 48-50). The edit distance between the two unique molecular identifiers can be 2 or more, which would equate to a Hamming distance of at least 2 (para. 141; instant claim 59).
In performing the method of Evans, consensus sequences can be generated using sets of strand reads, where the sets are compiled based on the similarity of their unique molecular identifiers (para. 194). When two sequencing adapters are used, the sequence identity of the read is also considered (para. 196). In this case, the sequences can also be aligned to a reference region (para. 197). As shown in Figures 8-9, when compiling consensus reads, errors in single reads that are introduced during amplification can be noted and removed (paras. 202-203). Figures 9B-9C show further ways to note errors arising from non-natural means (i.e. not true variants), and Evans states, “If the error was a true variant in the original duplex nucleic acid, then both Strand 1 and Strand 1′ would include the variant. Comparing the consensus sequence for Strand 1 with the consensus sequence for Strand 1′ allows for identification of an error at that position, as only one of the consensus sequences include the error,” (para. 204). Thus, Evans provides a way to distinguish between errors generated during amplification and mutants. True variants can be identified with the method of Evans, such as single nucleic polymorphisms (para. 181). Example 4 of Evans also shows the detection of SNPs (para. 661-662).
However, though Evans teaches that whole sequencing reads can be removed if they are thought to contain amplification or sequencing errors (e.g. para. 202), Evans does not teach trimming of the bases in each sequence read. It is noted that Evans also teaches that at least some of their adapter sequences can contain overhangs, which would be a sequence between a UMI and a target sequence (e.g. paras. 22, 52, and Figure 2).
Regarding claims 46 and 61, Peng teaches detection of variants using duplex UMIs in amplification and sequencing methods (Abstract). Single-end duplex-UMI adapters are used. These adapters are shown in Figure 1b, and are also noted to contain labels (the red “TT” and “GG” sequences, see page 3, para. 2). Note that the adapters have the UMIs in the middle of the reads, and the label on the top strand of the adapter is closer to the target sequence (Figures 1b-c). The labels function as labeling for individual strands, and provide enough information in a single strand to reliably identify a particular sequence (page 3, para. 2). These adapters are used during amplification (Figure 1c). On page 8, para. 3, it is stated that to process sequence reads, the adapters containing the UMIs and labels were removed from the reads. This process involves trimming the reads, as evidenced by the use of the phrase “trimmed reads” in line 3 of the paragraph. Because of the structure of the adapters of Peng, this trimming removes both sequences between the UMI and the sample sequence (e.g. the portion of the top strand adapter between the UMI and the sample), as well as the UMI, and the adapter sequence in general. As described above, such removal reads on step (d) of instant claim 46. The UMIs and labels were then used to tag the sequence reads for further analysis. The trimmed reads were then mapped to a reference genome, and UMI information was used to merge read families. The UMIs were then used as tags in the aligned reads. Consensus reads were then determined and variants were identified (page 8, “Read processing,” “Estimation of the panel-wise mean base substitution error rates,” and Figure 4). Peng teaches that their methods are particularly useful for duplex sequencing, which “has the superb ability in distinguishing real variants from various artifacts in the sample as well as [errors] introduced during the NGS workflow,” (page 5, para. 5). In particular, the UMI/label adapters had high specificity and uniformity, allowed for quicker sequencing compared to other methods, are highly accurate, and can distinguish very low level variants within a sample (page 6, para. 1).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the UMI/label adapter and processing methods detailed by Peng in combination with the consensus read determinations of Evans. Firstly, Peng details a duplex adapter that has a UMI followed by an additional label, and states that this structure is useful for individual strand identification. These adapters are placed before amplification. Evans also teaches adapters that may be placed on targets before amplification, and also teaches the use of duplex adapters containing UMIs. Thus, the ordinary artisan would be motivated to add the additional labels of Peng to the adapters of Evans in order to perform this individual strand identification. This would aid in determining the precise location of variants (or amplification/sequencing errors), providing more accurate results. This could then be applied to clinical decision making for particular variants, or aid in optimizing the amplification/sequencing methods if particular errors seem common, which may call for a redesign of primers/adapters or a change in reaction conditions. There would be a reasonable expectation of success with this addition as Peng specifically teaches that their adapter labels “can be easily made” (page 3, para. 2).
Additionally, the sequence read processing method of Peng (which involves the trimming of the exogenous adapters containing the UMI and label sequences) allows for determination of sequencing and amplification errors, and provides many benefits as stated above that would be of interest to the ordinary artisan. Both Evans and Peng teach similar methods for determining consensus sequences by organizing reads via UMIs. However, by trimming exogenous sequences off of sequence reads, as is done in Peng, and then later appending the UMIs and labels onto their appropriate sequences, this leaves the reads with much less noise in the form of primer or other sequencing adapter sequences, and allows for the ignoring of errors that may occur in these trimmed sequences but are not relevant to the results. MPEP 2143 I (A) states, “The rationale to support a conclusion that the claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art.” These processing methods of Peng still allow for the identification of variants via sequencing methods, and the combination of Evans in view of Peng would still result in the formation of consensus sequences while identifying sequence errors that can occur during amplification and sequencing, thereby producing predictable results. There would also be a reasonable expectation of success for the ordinary artisan as combining these methods would simply add an additional sequence to the adapters of Evans (whose generation is taught step-by-step in Peng), as well as add an additional downstream analyses to the method of Evans that would not affect the adapter design or the amplification and sequencing methodologies of the reference.
Thus, claims 46-52, 54, and 59-61 are prima facie obvious over Evans in view of Peng.
Regarding claim 53, Evans does not explicitly teach how long the non-barcode duplex regions of their adapters (i.e. the yoke regions) may be. However, the reference does generally teach that the barcodes may be of any length, and provides specific teachings of 2-24 bases in length (para. 143). In the provided examples, the molecular barcodes were 12-14 nucleotides in length (paras. 653-654 and 656). From these teachings, it would be prima facie obvious to make the yoke regions of the adapters around or shorter than 10-12 bases in length in the method of Evans in view of Peng, depending on the length of the region between the UMI and the sample nucleic acid, as this would still keep the entire duplex region (with the barcode, label, and yoke sequences) under the taught length of 24 nucleotides, while also allowing for barcodes of a length typically taught in Evans. This length of barcode is shown by Evans to be successful (e.g. 653-655 and 656-658), and so the ordinary artisan would be motivated to use said length, and by making the yoke region of such a length as to keep the entire duplex region under the stated maximum for the barcode in particular embodiments, this can ensure that no adverse effects related to adapter length are seen in the method of Evans in view of Peng.
Thus, claim 53 is prima facie obvious over Evans in view of Peng.
Claims 55-58 and 62-65 are rejected under 35 U.S.C. 103 as being unpatentable over Evans et al. (US 2017/0355984 A1), in view of Peng et al. (Nature Scientific Reports, 2019), and further in view of Zhao et al. (US 2019/0085384 A1).
Evans in view of Peng teaches the methods of claims 46-54 and 59-61, as noted above. Evans also teaches that a variety of barcodes (UMIs) may be used (e.g. the 96 barcodes of para. 97 and Figure 3) and teaches that the balance of nucleotides among a given set of barcodes can be relatively equal (para. 148 and Figures 4-5). Evans also teaches the use of a large range of unique molecular identifiers, from 2 to 384 (para. 140). However, neither Evans nor Peng explicitly teaches the specific UMIs shown in instant claims 55-58 and 62-65.
Zhao teaches methods for making and using UMIs to determine sequences of interest (Abstract). Zhao particularly focuses on non-random UMIs, which are predefined for a particular application, and rules can be used to generate particular UMI sequences, such as where the sequences can differ by a particular number of nucleotides (e.g. 2, 3, or 4; para. 74). Zhao teaches that UMIs can be 5 base pairs long (para. 324), and the references also provides examples of UMIs that are 6 and 7 nucleotides in length (paras. 74 and Table 4). Many of the sequences in Table 4 comprise the claimed UMI sequences – for example, CTAAGGA, AAGGATG, GACAAC, CCGATA, TCGTGTG, ATTGTCG, and CTTGGC, where the bolded portions show the claimed UMI sequences. Thus, Zhao explicitly teaches utilizing 6 of the UMIs recited in the instant claims. It is noted that the instant claims state the UMIs may comprise the listed sequences, and so can include additional nucleotides. Zhao also teaches elsewhere in the reference that UMI sequences may be 5-7 nucleotides in length (para. 77). Zhao further teaches additional selection criteria for the set of UMIs, including wherein the set of UMIs excludes sequences having three or more consecutive identical bases, excludes sequences having a combined number of guanine and cytosine bases smaller than 2 and larger than 4, excludes sequences having a same base at the last two positions, and excludes sequences having a thymine base at the last position (paras. 16-19). Zhao further teaches that these UMIs are configured to identify individual nucleic acid molecules in a sample for multiplex massively parallel sequencing (para. 4), and teaches that purposefully designed, non-random unique molecular identifiers allow for simpler manufacturing (para. 168).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the UMI criteria established by Zhao in the method of Evans in view of Peng. Evans and Zhao teach very similar adapter structures (e.g. see Figure 1B of Zhao and Figure 1A of Evans) but Evans does not explicitly teach particular UMI sequences. Zhao teaches deliberate rules for creating UMIs that would lead to successful use by the ordinary artisan, and so the ordinary artisan would be motivated to use the design criteria described by this reference. MPEP 2143 I (B) states, “The rationale to support a conclusion that the claim would have been obvious is that the substitution of one known element for another yields predictable results to one of ordinary skill in the art.” Substituting the UMI structure of Zhao for that of Evans in view of Peng would yield predictable results, as said result would simply be known UMI sequences that could be used for grouping sequence reads, as is done in Evans in view of Peng. As noted above, Zhao teaches the use of 6 of the specifically claimed UMI sequences. A UMI with 5 nucleotides would have a possible 1,024 combinations, a UMI with 6 nucleotides would have a possible 4,096 combinations, and a UMI with 7 nucleotides would have a possible 16,384 combinations (utilizing the logic from Zhao para. 74). Using all or some of the selection criteria of Zhao would further limit the number of possible UMIs that can be used. As there are a finite number of UMIs that can be created, it would be obvious to one of ordinary skill in the art to develop other sequences beyond the ones explicitly enumerated by Zhao and to arrive at the other sequences listed in instant claims 55-58 and 62-65 that are not explicitly taught by Zhao - this would be a simple substitution of one UMI for another. It is also noted that no evidence of critical or unexpected results for the use of a particular UMI sequence has been described by Applicant. Additionally, it would have been obvious to one of ordinary skill in the art to select a set of unique molecular identifiers as taught by Zhao, as Zhao teaches that purposefully designed non-random UMIs allow for simpler manufacturing. Ten or more unique molecular identifiers could be used in this set, in accordance with the guidance provided by Evans.
Thus, claims 55-58 and 62-65 are prima facie obvious over Evans, in view of Peng, and further in view of Zhao.
Conclusion
No claims are currently allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681