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. Claim 23 has been canceled. Claims 1-6, 8-21, 24-31, and 33-36 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Claim Objections
Claims 1, 13, 15, and 30 were objected to due to minor informalities. In light of Applicant’s amendments to the claims submitted 7/10/2026, these objections have been withdrawn. However, see new grounds of objection below.
35 USC 112(b) Rejections
Claims 6 and 23 were rejected for various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 7/10/2026, the rejection for claim 6 has been withdrawn. Claim 23 has been canceled, and so this rejection has been rendered moot.
35 USC 112(d) Rejections
Claim 23 was rejected for being of improper dependent form. This claim has been canceled, and so this rejection has been rendered moot.
35 USC 103 Rejections
Claims 1-6, 8-21, 23-31, and 33-36 were rejected under 35 U.S.C. 103 as being unpatentable over Seitz et al. (US 2017/0342409 A1).
Applicant’s arguments and amendments have been thoroughly reviewed and considered. The rejections for claims 1-6, 8-21, 24-31, and 33-36 have been maintained. See “Response to Applicant’s Arguments” below. Claim 23 has been canceled, and so this rejection has been rendered moot.
Response to Applicant’s Arguments
Regarding the 35 USC 103 Rejections, Applicant argues that Seitz, the primary reference, does not teach an identification sequence that does not hybridize to the elongation stopper or the nucleic acid template, where said identification sequence remains single-stranded and not hybridized (Remarks, page 9). Specifically, Applicant argues that Seitz teaches an identification sequence that is hybridized to an elongation stopper. Applicant states that the teachings of Seitz in paras. 103 and 156 refer to 3’ ends of sequences, and so cannot read on the identification sequence of the claims, which require a 5’ identification sequence (Remarks, page 10). In using the teachings of Seitz, Applicant argues that the Examiner uses hindsight reconstruction, and is generally improper, as Seitz allegedly teaches away from the claimed invention (Remarks, pages 10-11). Finally, Applicant argues regarding the use of the term “free” or “free ends” in Seitz, and that the interpretation of these terms used in the rejection is not the intended interpretation of the reference (Remarks, page 11).
Regarding the teachings of Seitz, paras. 103, 156, and Figure 8f were used to provide general teachings regarding overhangs/portions of sequences that are not hybridized to another sequence in the reference. The Examiner agrees that the reference does not clearly state that a 5’ portion on a tag/linker can be used, and as much is stated in para. 33 of the Non-Final Rejection (“However, it is not clear that the tag/linker can contain a 5’ portion that does not hybridize to the stopper.”).
Regarding para. 34 of the Non-Final Rejection, the Examiner agrees that the rationale used to create this obviousness rejection is not wholly based on reasoning found in Seitz. However, according to MPEP 2144, this is not a requirement for a conclusion of obviousness. Section I states, "The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992); see also In re Kotzab, 217 F.3d 1365, 1370, 55 USPQ2d 1313, 1317 (Fed. Cir. 2000) (setting forth test for implicit teachings); In re Eli Lilly & Co., 902 F.2d 943, 14 USPQ2d 1741 (Fed. Cir. 1990)." Additionally, MPEP 2141.03 states, ""A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton." KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 421, 82 USPQ2d 1385, 1397 (2007). "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle." Id. at 420, 82 USPQ2d 1397. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ." Id. at 418, 82 USPQ2d at 1396."
In para. 34 of the Non-Final Rejection, the teachings of Seitz are used with knowledge, skill, and creativity available to the ordinary artisan, and it is the Examiner's opinion that the ordinary artisan would be capable of putting these factors together to arrive at the claimed invention, even though Seitz may not explicitly anticipate every limitation in the claimed invention. The reasoning of para. 34 of the Non-Final Rejection is as follows - “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… 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.” This rationale for producing 5’ overhangs naturally stems from the teachings of Seitz regarding labeling/identification sequences and the operation of the elongation stopper and subsequent ligation, as well as general knowledge about sequence specificity and barcodes. None of this latter knowledge would be impossible or improbable for the ordinary artisan to obtain.
In relating this to impermissible hindsight, MPEP 2145 X (A) states, “However, "[a]ny judgment on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant’s disclosure, such a reconstruction is proper." In re McLaughlin, 443 F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971).” No portion of Applicant’s disclosure is cited in the explanation of rationale made by the Examiner, and it is unclear what particular knowledge would only be found in Applicant’s disclosure and would not readily be available to the ordinary artisan otherwise.
At the top of page 11 of their Remarks, Applicant cites para. 79 of Seitz as evidence of teaching away from the claimed invention and the Examiner’s proposed modification. It is unclear how precisely this paragraph teaches away from the claimed invention. MPEP 2145 X (D) 1 states, “Furthermore, "the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004).” This paragraph of Seitz provides details on a particular embodiment, and does not disparage other embodiments or possibilities. Furthermore, it is unclear how including a 5’ identification sequence on the L2 tag sequence of Seitz would lead the ordinary to not expect that ligation between the tag and the elongation product would be possible. See Figure 4 of Seitz below, labeled for clarity:
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As already described in Figure 4 of Seitz, the L1/Pn elongation product is elongated until it reaches the stopper sequence (the Sm sequence with attached L2rc), and then the elongation product is ligated with L2. The junction of the elongation product, elongation stopper, and tag is circled in red. In the modified version of Seitz presented in the Non-Final Rejection, an identification sequence added as a 5’ overhang to the L2 tag sequence would be added to the circled region shown above in Figure 4, and thus would be in the same proximity to the elongation product as the unmodified L2 sequence in the figure. Thus, there would be a reasonable expectation of success that the ligation of the elongation product with the L2 sequence would still be possible.
Regarding the “free ends” discussion on page 11 of Applicant’s Remarks, the Examiner did not rely on any particular interpretation of “free ends” in Seitz when forming the Non-Final Rejection. In para. 34, the Examiner states, “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.” This is not to say that the majority of the L2 sequence would not be hybridized to the stopper or template sequence, as even the very 5’ end of L2 is hybridized to the stopper in Figure 4 of Seitz. However, by the very logic and nature of the overhang sequence presented in the rejection, this overhang is a unique sequence that can act as a label/identifier, and so thus does not hybridize to the stopper or template sequence, as it would be distinctly designed. This conclusion is not based on recitations involving free 5’ ends.
Thus, Applicant’s arguments are not considered persuasive to overcome the prior art rejections of record, and these rejections have been maintained and are reiterated below.
Claim Objections
Claim 6 is objected to because of the following informality: to clearly link the limitations described in claim 6 with those of claim 1, it is recommended that the claim read, “The method of claim 5, wherein the elongation stopper anneals to the template nucleic acid via an annealing sequence, wherein said annealing sequence is a random sequence,” or similar language. Appropriate correction is required.
Claim 30 is objected to because of the following informality: in line 2, “amplification fragment” should read “amplification fragments.” Appropriate correction is required.
Claim 31 is objected to because of the following informality: one or more elongation stoppers is recited in lines 1-2 of the claim. The claim then states “on its 3’ end,” referring to the 3’ end of the elongation stoppers. It is thus recommended for “on its 3’ end” to read “on its/their 3’ end,” or for the final phrase to read “priming an elongation reaction on the 3’ end of the one or more elongation products,” or similar phrasing. Appropriate correction is required.
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, 24-31, 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 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.
THIS ACTION IS MADE FINAL. 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 FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
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/F.F.G./Examiner, Art Unit 1681
/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
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