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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 3/16/2026 has been entered.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 7, 22, and 32 have been canceled. Claim 36 has been added. Claims 1-6, 8-21, 23-31, and 33-36 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Claim Objections
Claims 1 and 14 were objected to due to minor informalities. In light of Applicant’s amendments to the claims submitted 3/16/2026, these objections have been withdrawn. However, see new grounds of objection below.
35 USC 102 Rejections
Claims 1, 5-6, 8-11, 13, 21-28, and 35 were rejected under 35 U.S.C. 102(a)(1) as being anticipated by Seitz et al. (WO 2013/038010 A2). In light of Applicant’s amendments to the claims submitted 3/16/2026, these rejections have been withdrawn for all currently pending claims. See “Response to Arguments” and new grounds of rejection below. Claim 22 has been canceled, and so this rejection has been rendered moot.
35 USC 103 Rejections
Claims 2-4, 7, 12, 14-19, 20, and 29-34 were rejected under 35 U.S.C. 103 as being unpatentable over Seitz et al. (WO 2013/038010 A2). In light of Applicant’s amendments to the claims submitted 3/16/2026, these rejections have been withdrawn for all currently pending claims. See “Response to Arguments” and new grounds of rejection below. Claims 7 and 32 have been canceled, and so these rejections have been rendered moot.
Response to Applicant’s Arguments
Regarding the 35 USC 102 Rejections presented in the Final Rejection mailed 9/17/2025, Applicant argues that the teachings of the reference do not anticipate each element of claim, and disagrees with the Examiner’s interpretation of the teachings of Seitz, the primary reference used. Specifically, where Sm (the elongation stopper), is not part of the ligated product in Figure 4. Applicant states that, “Sm would not be in the final product because L2rc is not in the final product,” and argues that the stopper, as stated by Seitz, comprises both Sm and L2rc. Additionally, Applicant argues that Seitz does not teach the newly amended limitation of the claim that states that the identification sequence remains single stranded and not hybridized (Remarks, pages 9-10).
Regarding the amendments to claim 1, “wherein the adaptor nucleic acid is not bound to the elongation stopper,” this is noted to not substantially limit the claim to only this embodiment, as this wherein clause is stated in the alternative with the previous wherein clause (“wherein a part of the adaptor nucleic acid hybridizes to the elongation stopper or to a part thereof, or wherein the adaptor nucleic acid is not bound to the elongation stopper”). Additionally, Applicant’s amendments to remove the “in case” language now limit the claim to one of the alternative options and limit the identification sequence to remaining single stranded and not hybridized.
In determining the ability of a prior art reference to read on the instant claims, the teachings of the prior art are evaluated in light of their ability to map onto the limitations of the instant claims, based on the broadest reasonable interpretation of the terms in the instant claims. Regarding an “elongation stopper” in the instant claims, on page 8 of the instant specification, it is stated, “In essence, such a stopper stops the elongation reaction of an upstream elongation reaction…by presenting an obstacle on the template.” The term “elongation stopper” is thus generally used to refer to a sequence that hybridizes to a template in order to stop an elongation reaction of any kind.
In relating this interpretation to the teachings of Seitz, it is irrelevant as to whether Seitz itself calls Sm alone or Sm and L2rc together an elongation stopper. The sequence of Sm is the sequence that hybridizes to a target to stop elongation, and so this sequence was considered analogous to the claimed elongation stopper in the Final Rejection. The elongation stopper of the instant claims has no requirements or restrictions for additional structural elements that may be attached to said stopper, and so the existence of the L2rc sequence bound to the stopper Sm did not obviate the use of Sm alone as being analogous to the elongation stopper.
Regarding the 35 USC 102 Rejections in relation to the currently amended claims, the specific teachings of Seitz referenced and mapped to claim 1 do not teach the required features of the adaptor in the newly amended portion of the claim, nor that the identification sequence remains single stranded and not hybridized. Thus, new grounds of rejection are found below.
Claim Interpretation
For clarity of the record, interpretations of the following claim elements are provided (note that all paragraph citations refer to the corresponding paragraphs in the application as published):
“Elongation stopper” – as noted above, no specific definition of this term has been provided. Para. 27 states that stoppers are preferably DNA, and para. 29 notes that stoppers are nucleic acids that anneal to template nucleic acids downstream of elongation products to stop elongation reactions. Para. 29 also states, “In essence, such a stopper stops the elongation reaction of an upstream elongation reaction (hence , the stopper is downstream of the elongation product) by presenting an obstacle on the template. The stopper is annealed or hybridized to the template and the elongation reaction does not displace the stopper and thus aborts.” Thus, the elongation stopper will be considered any nucleic acid that can perform this function, with no specific structural requirements for such a sequence.
“Adaptor” - Para. 27 states that adaptors are preferably DNA, and para. 31 notes that adaptors have identification sequences on their 5’ ends. No additional specific requirements appear to be recited, and so adaptors will be considered to be any nucleic acid sequence with an identification sequence at its 5’ end.
“Identification sequence” – Para. 31 notes that this sequence is “used for the 5' terminal part of the adaptor nucleic acid that is not hybridizing or annealing - even if only parts of the identification sequence would later be used for identification.” Thus, this sequence will be considered any nucleic acid sequence that meets these requirements that can be used for identification, with no actual identification required. It is note that para. 37 states that identification sequences can be random, and can be identified by their position relative to the rest of the adaptor.
It is noted that in the instant invention, the terms “hybridizes” and “bound” are used to refer to the relationship of sequences to one another. In the claims, these terms are interpreted with “hybridizes” having the typical meaning in the art and “bound” meaning that a sequence can be attached to another sequence. It is noted that “bound” is not specifically defined in the instant specification, but in para. 42 of the application as published, distinctions are made between adaptor nucleic acids being “bound, hybridized to, or is/are not bound to.” This indicates that hybridizes and bound are intended to be used differently by Applicant. Later in this paragraph, sequences are described as “bound or hybridized” to one another, indicating that “bound” does not mean “hybridized.” As nucleic acid sequences, when interacting with one another, may generally be either attached or hybridized to one another, “bound” is thus interpreted as being similar to “attached,” particularly in light of the fact that Applicant does not teach the use of secondary structures (e.g. hairpins) with their claimed nucleic acid features.
Claim Objections
Claim 1 is objected to because of the following informalities: in line 2 of the final phrase, “for ligation the elongation products are hybridized to” should read “for ligation the elongation product is hybridized to,” as only a single elongation product is recited earlier in the claim. Appropriate correction is required.
Claim 13 is objected to because of the following informalities: in line 2, “elongating the at least two…” should read “wherein the elongation comprises elongating the at least two…,” and the word “and” should be inserted before the final “wherein” in line 3. Appropriate correction is required.
Claim 15 is objected to because of the following informality: a comma should be inserted after “The kit of claim 14.” Appropriate correction is required.
Claim 30 is objected to because of the following informality: the word “segments” in line 2 should be removed to better match the language of claim 12, from which this claim depends. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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.
Claims 6 and 23 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.
Claim 6 recites the limitation “the annealing sequence” in line 1. There is insufficient antecedent basis for this limitation in the claim, as neither this claim, nor claims 1 and 5, from which this claim depends, recite the use of “an annealing sequence.” Furthermore, it is unknown to which element of claim 1 this annealing sequence belongs. It will be interpreted as though this refers to the portion of the elongation stopper that is annealed to the template nucleic acid.
Claim 23 is rejected because the scope of the claim is indefinite. Firstly, the claim depends on claim 7, which has been canceled. Secondly, the claim describes a scenario in which “the adaptor nucleic acids are bound to the elongation stoppers.” This phrase: 1) recites multiple adaptor nucleic acids when only “an adaptor nucleic acid” is recited in claim 1, and 2) presents an option for the adaptor nucleic acid’s interaction with the elongation stopper that is not presented in claim 1. It will be interpreted as though this claim depends on claim 1, and requires that the adaptor nucleic acid of claim 1 have an identification sequence that is generally independent of an annealing sequence of the elongation stopper.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 23 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 23 is rejected as it is of improper dependent form. Specifically, this claim depends on claim 7, which has been canceled. Proper dependent claims must depend on a claim previously set forth. See MPEP 608.01(n) III.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 1-6, 8-21, 23-31, and 33-36 are rejected under 35 U.S.C. 103 as being unpatentable over Seitz et al. (US 2017/0342409 A1).
Seitz teaches methods for generating an amplified nucleic acid portion of a template nucleic acid (Abstract). One such method (para. 24) comprises:
Providing a template nucleic acid.
Annealing a first oligonucleotide primer to said template nucleic acid.
Annealing at least one further oligonucleotide primer to said template nucleic acid.
Elongating the first oligonucleotide primer in a template specific manner until it reaches the further oligonucleotide primer. Here, the further oligonucleotide primer can act as a stopper, and can be elongated itself, also acting as a primer.
This thus meets the requirements of the first three clauses of instant claim 1. Seitz also teaches the use of sequence tags that can be attached to elongation products (e.g. para. 62). In para. 104, it is stated that elongation stoppers may be hybridized with tags that act as labels. These tags can be positioned so that their 5’ ends are near the 3’ end of an elongation product of an upstream primer so that ligation of the tag and elongation product can occur. Such a setup is shown in Figures 4 and 7i (where the tag would be L2). These tags are also referred to as linkers.
However, it is not clear that the tag/linker can contain a 5’ portion that does not hybridize to the stopper. In para. 103, it is stated that 5’ overhangs are possible for hybridized sequences that do not participate in the primer extension reaction, and para. 156 notes that in at least some embodiments, L2 sequences may have a portion that does not hybridize to any structure (see Figure 8f). Also generally, Seitz teaches that tags can be used for identification of amplification products, particularly in downstream sequencing applications (para. 64).
Thus, 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 combine the teachings of Seitz to arrive at the invention of instant claims 1 and 35-36. Specifically, the ordinary artisan would recognize that by adding a 5’ overhang to the L2 sequence tag, this would allow for a portion of said tag to not be hybridized to the stopper sequence, and this increased length would allow for potentially easier ligation of the adaptor with an elongation product. Additionally, Seitz teaches that sequence tags can be used for labeling, detecting, or recognizing particular sequences that they are labels for (paras. 78-79). Sequence tags are also taught in the same context as barcodes by Seitz (e.g. paras. 62 and 64). Given that these sequence tags are being ligated to elongation products, they are thus being used to label said products. Most of the sequence of the sequence tag is hybridized to the elongation stopper, and thus may dictated by the sequence of said stopper. By including an overhang sequence, this sequence can also act specifically as a barcode/identification sequence, with no limits or restrictions on the structure of said sequence. This would be particularly helpful for labeling contexts, as particularly elongation products can be particularly labeled or grouped, which can aid in identifying particular targets for further analyses. There would be a reasonable expectation of success in creating this overhang as Seitz teaches that 5’ overhangs are possible and teaches embodiments in which sequencing tags are not totally complementary to another sequence. Additionally, this overhang would not interfere with the broader hybridization/elongation methods of Seitz taught above. It is noted that this overhang identification sequence would not hybridize to any other sequence upon ligation with the extension product, and would remain single-stranded, as the elongation product itself would be single-stranded.
Thus, claims 1 and 35-36 are prima facie obvious over Seitz.
Regarding claims 2 and 17-19, Seitz also teaches the creation of a cDNA library that does not include an elongation stopper, where the elongation of at least one oligonucleotide primer is able to reach the 5’ end of the template nucleic acid (the description of Figure 2 in para. 150). Ligase is also shown to be involved in these methods (Figure 2). Seitz also notes that linkers (similar to the tags described above) can be ligated to any amplified nucleic acids of their invention (para. 89), and generally teaches that linkers can be ligated to elongated nucleic acid products (para. 90). In this latter teaching, though an elongation stopper is used as an example, it is not required. These linkers can thus be analogous to the adapters in the instant claims. This reference also teaches that M-MLV reverse transcriptase can be used, and that terminal transferase activity can add nucleotides to amplified fragments resulting from the invention (paras. 136 and 138). Therefore, it would be prima facie obvious for one of ordinary skill in the art to combine these aspects to create an embodiment of Seitz where no elongation stopper is required, an adapter is added after elongation, and nucleotides are added to fragments after amplification. The ordinary artisan would be motivated to do this because the exclusion of the oligonucleotide stopper would mean less resources are required for the overall method, and Seitz teaches that by adding nucleotides to amplified fragments, single-stranded products can more quickly and efficiently hybridize to a template, which would be useful for downstream analyses (para. 138). In adding the linkers/adapters, Seitz teaches that linkers are particularly useful for amplification and next generation sequencing methods, and so including these adapters even in the absence of an elongation stopper would aid in downstream analyses (para. 89).
Regarding claims 3 and 20, in Seitz, sequence tags are unique, pre-selected nucleic acid sequences that can be used to detect, recognize, or amplify a sequence labelled with said tag (paras. 78-79). Because the sequence tags are taught to be hybridized to a portion of the oligonucleotide stopper (the L2rc sequence), and Seitz teaches that at least 50 distinct stoppers and 50 distinct oligonucleotide primers can exist (para. 63-64), then at least 50 sequence tags can exist and be ligated in the method described above in the rejection of claim 1. It would also generally be prima facie obvious to one of ordinary skill in the art to create unique sequence tags (which would include different identification sequences) in order to detect particular sequences, and to correspond to the unique stopper sequences. This would be particularly useful if the ordinary artisan wanted to only detect fragments from a particular region of a template nucleic acid, such as those corresponding to potential mutation and/or disease-related regions.
Regarding claim 4, Seitz also teaches that the oligonucleotide primer/stopper sequences may be random sequences, and also teaches the synthesis of random sequences (paras. 28 and 63-64). As the identification sequence on the sequence tag is an overhang sequence, the sequence tags of Seitz are unique, pre-selected nucleic acid sequences that can be used to detect, recognize, or amplify a sequence labelled with said tag (paras. 78-79), and Seitz provides evidence that synthesis and use of random sequences is possible with their methods, it would be prima facie obvious for one of ordinary skill in the art to additionally randomly synthesize the identification sequence of the sequence tag. This would ensure that every elongation product labeled with the identification tag is distinctly labeled, and thus can be individually detected. This would be particularly useful for downstream methods involving identifying particular amplicons/sequence reads or groups of amplicons/reads, as each read could be distinguished from one another, which may aid in analyses of mutations. Additionally, this would allow the identification sequence to be distinguished from any primer, stopper, or additional adaptor/tag sequence in the amplicons or sequence reads.
Regarding claims 5-6 and 21, as noted above in the rejection of claim 1, in para. 24 Seitz notes that elongation stopper sequences can be elongated themselves, thus also acting as primers. Seitz teaches that anywhere from 1-50 oligonucleotide stoppers may be used in the invention, where these different stoppers may differ in their annealing sequences, and the annealing sequences may be random (para 64). Though the stoppers in para. 64 are not necessarily of the same embodiment as those in para. 24, it would be prima facie obvious that as Seitz teaches that multiple stoppers can be used in para. 64, each of these stoppers could perform the functions taught by Seitz elsewhere in their invention, so long as the stoppers did not interfere with one another. This lack of interference would be accomplished via different annealing sequences that were sufficiently far from one another so that overlaps between stoppers would not be possible. As Seitz teaches the use of different annealing sequences, implying these annealing sequences are distinctly designed and chosen for use together, such a design would be possible for the ordinary artisan to develop.
Regarding claims 8 and 24, Seitz teaches that the template nucleic acid is preferably RNA, which is elongated via reverse transcriptase (paras. 20, 25, 28, 47, and 57).
Regarding claims 9 and 25, the instant specification states that “a universal sequence means that it is the same for all primers, stoppers or adapters, respectively,” (page 17, line 38 through page 18, line 2). Thus, these claims are interpreted to mean that all primers or adaptors comprise the same sequence (in the claim of instant claim 9) and/or that all elongation stoppers comprise the same sequence (in the case of claim 25). As noted in the rejections above, all of the primers, stoppers, and tags of Seitz may be used for elongation/amplification, and thus a universal sequence on each of them would be considered a ”universal amplification sequence”/”universal adaptor amplification sequence.” For claim 9 specifically, para. 62 notes that if different elongation products are labeled with the same sequence tag, this is useful for further amplification or sequencing applications. Thus, it would be prima facie obvious to have the sequence tags contain the same, universal, sequence. In paras. 63-64, it is stated that as few as one distinct primer or stopper may be used. In these embodiments, as the stoppers and primers would all comprise the same sequence (within each group), these would therefore also be considered universal sequences.
Regarding claims 10 and 26, Seitz teaches that in a preferred embodiment where the template nucleic acid is specifically mRNA, oligo dT primers can be used to anneal to the poly A tail of the mRNA. The oligo dT primer can include anchored oligonucleotides (para. 127).
Regarding claims 11 and 27-28, Seitz teaches that the ligation reaction can include PEG and Tween (paras. 73-74) and also teaches that oligonucleotides may be modified to increase their melting temperature (para. 105). These modifications specifically refer to oligonucleotides that bind to the template strand, and therefore encompass the elongation stopper and oligonucleotide primer (para. 105).
Regarding claim 12, this claim overlaps in scope with claims 3/20 (which requires a plurality of adaptor nucleic acids with different identification sequences) and claim 5 (where the elongation stopper has primer activity and is also elongated), along with the additional limitations described in the further comprising clause of the claim. Because the sequence tags can be used to aid in amplifying a sequence labelled with said tag, it would be prima facie obvious to further amplify the elongation products (which are amplification fragments, as they are copies of template sequences) with said sequence tags (e.g. para. 62; instant claim 30). Seitz also teaches creating a sequence library with the generated amplified fragments (para. 27), and that tags on amplification products may be used for identification in such a sequence library (paras. 62 and 64).
Regarding claim 29, which depends on claim 12, as noted above in the rejection of claim 3 (and claim 20), the use of up to 50 distinct sequence tags (with distinct identification sequences) is obvious in view of Seitz.
Regarding claim 13, Seitz teaches that anywhere from 1-50 oligonucleotide primers may be used, where elongation of said additional primers may also be stopped with an elongation stopper (para. 63).
Regarding claims 14 and 16, Seitz teaches a kit for performing their method (para. 28). This kit comprises a reverse transcriptase, a ligase, oligonucleotide primers, and oligonucleotide stoppers. Kits of the invention can also include carrier means and the necessary tools for holding reagents (e.g. vials), and can include oligo dT primers specifically (para. 146). Though this recitation does not explicitly include sequence tags, it would be prima facie obvious for the ordinary artisan to include them in order to create a kit that can fully perform the method of Seitz described by claim 1, and so that reaction products can be more easily detected and identified (para. 79). This would also allow for better commercial success of such a kit, as each basic element required to perform the method of Seitz would be found in the same location.
Regarding claims 15 and 33, Seitz specifically teaches that the kits can have more than one primer or stopper (para. 28). This reference also teaches that the invention may comprise up to 50 distinct primers and 50 distinct stoppers (paras. 63-64). In order to ensure each elongation product is distinctly labelled, the same number of sequence tags and primers would be needed. Therefore, it would be prima facie obvious for the ordinary artisan to also include up to 50 distinct sequence tags in the kit of Seitz. The use of 50 distinct sequence tags/identification sequences would also ensure that each elongation product can be distinctly labeled, which can aid in detecting and identifying particular sequences of interest.
Regarding instant claim 23, in Seitz, the tag L2 sequence that is bound to the L2rc region of the elongation stopper acts independently of the stopper annealing sequence to the template (see Figure 4 and 7i), and thus, this independence would apply to the sequence tag in the teachings of Seitz described above in the rejection of instant claim 1.
Regarding claim 31, Seitz teaches that the elongation stopper can also act as an initiator of elongation itself, thereby acting as a primer (para. 24). This elongation would be at the 3’ end (see for example the orientation of the stopper Sm in Figure 4). As stoppers are generally recited in the kits of Seitz, it would prima facie obvious that all iterations of stoppers taught by the reference could be included in said kits.
Regarding claim 34, Seitz renders obvious the kit of claim 16, as described above, and teaches that the oligo dT primer can include anchored oligonucleotides (para. 127).
Conclusion
No claims are currently allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
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/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
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