DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. 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
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 19 December 2025 has been entered.
Claim Rejections - 35 USC § 102
3. 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.
4. Claims 1, 8, 9, 10, 15, 17, 21, 27, 28 and 39-41 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Gu et al (United States Patent Application US20180230516, published 16 August 2018).
Regarding claim 1, Gu teaches a method of producing a nucleic acid library comprising the ligation of adapters to the 5' and 3' ends of a single-stranded target nucleic acid (abstract). Gu teaches that the first adapter comprises a first oligonucleotides and a plurality of first scaffold polynucleotides hybridized together, and the second adapter comprises a second oligonucleotide and a plurality of second scaffold polynucleotides hybridized together (FIG 1). Gu teaches that the first and second adapters are hybridized to a first and second end of a first and second ssNA terminal region, thereby forming a hybridization product in when an end of the first oligonucleotide and an end of the second oligonucleotide are adjacent to different ends of the first ssNA (FIG 1). Gu teaches that these components are all combined in a single reaction ([0014] and [0313]). Gu teaches ligating (i.e., covalently linking) the 3' and 5' adapters to the terminal ends of the target nucleic acid (FIG 1, [0314]), and that the ligation products are reverse transcribed, amplified, and sequenced ([0024]). It is noted here that the amendments to claim 1 recite “sequencing the covalently linked hybridization products or amplification products thereof.” The broadest reasonable interpretation of “…amplification products thereof” as they relate to an RNA target would include amplified cDNA products generated from an RNA.
Regarding claim 8, Gu teaches adding a mixture of single stranded oligonucleotides to a double stranded 5' adapter and a double stranded 3' adapter.
Regarding claim 10, Gu teaches ligating the 3' and 5' adapters to the terminal ends of the target nucleic acid using an RNA ligase (FIG 1, [0314]).
Regarding claims 15 and 17, Gu teaches that the adapters comprise random single-stranded overhangs that hybridize to the target ssNA ([0280]). Having random single-stranded overhangs as taught in Gu inherently means that the ssNA hybridization region of each polynucleotide of the first and second polynucleotide species is different than the ssNA hybridization region of other first and second polynucleotide species.
Regarding claims 21 and 27, Gu teaches that the 3' adapter comprises a di-deoxy nucleotide at the 3' termini to minimize self-ligation ([0042] and SEQ ID No: 5 in [0280]). This embodiment corresponds to the limitation of claim 21 (2) wherein the second oligonucleotide comprises one or more modified nucleotides (ddC), wherein the one or more modified nucleotides are capable of blocking covalent linkage (i.e., ligation) of the oligonucleotide to another oligonucleotide (i.e., a ligation blocking modification).
Regarding claim 39, Gu teaches that the target nucleic acid is a single-stranded RNA ([0014], [0015] and FIG 1).
Regarding claims 40 and 41, Gu teaches methods of small RNA library preparation including enrichment ([0209] – [0220]) and adapter ligation ([0225] – [0230]). None of these steps disclose or require the modification of the small RNA or the ends of the small RNA.
Claim Rejections - 35 USC § 103
5. 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.
6. 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.
7. Claims 1, 6, 8, 10, 15, 17, 21, 27-28, and 39 are rejected under 35 U.S.C. 103 as being unpatentable over Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018).
Regarding claim 1, Raine teaches a nucleic acid composition comprising single-stranded nucleic acid (FIG 1. SPLAT diagram, bisulfite conversion sample and [0060]), a first oligonucleotide, and a plurality of first scaffold polynucleotide species (FIG. 1 SPLAT diagram, reference 180 and [0104]). Raine teaches a plurality of scaffold polynucleotides comprising an ssNA hybridization region (i.e., a 3' random overhang [0104]) and a first oligonucleotide hybridization region (i.e., the short double-stranded region [0060]). Raine teaches that the double stranded adapter is annealed to the 3' ends of the ssDNA library, i.e., forming hybridization products in which an end of the molecule of the first oligonucleotide is adjacent to an end of the first ssNA terminal region ([0104]). Raine does not teach that the ssNA is combined with a single-stranded binding protein (SSB) prior to the combining or during the combining. Raine additionally teaches combining the nucleic acid composition with a second oligonucleotide and a plurality of second scaffold proteins (FIG. 1, reference 184 and [0104]). Raine teaches a second step wherein the 5' ends of the ssDNA are ligated to adapters comprising a random 5' overhang (i.e., forming hybridization products in which an end of the molecule of the second oligonucleotide is adjacent to an end of the second ssNA terminal region [0104]).
Raine does not teach that a first oligonucleotide and plurality of first scaffold species, the second oligonucleotide and the plurality of second scaffold species, and the single-stranded nucleic acid are combined in a single reaction.
However, Gu teaches a target RNA hybridized to a pair of partially double-stranded adapters (FIG 1) and Gu teaches that these components are all combined in a single reaction ([0014] and [0313]).
It would have been obvious to one having ordinary skill in the art to having modified the sequential method taught by Raine with the one-pot reaction method taught by Gu to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to reduce sample loss due to purification or transfer between reaction vessels. In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited methods predictably result in the ligation of 5' and 3' splinted adapters to a single-stranded target nucleic acid.
Regarding claim 8, Raine teaches short double stranded adapters comprising a random 3' or 5' overhang are annealed to the 3' or 5' ends of the ssDNA library, i.e., the scaffold polynucleotide species (comprising the random 3' or 5' overhang) is hybridized to a first or second oligonucleotide forming a plurality of first and second scaffold duplex species ([0104]).
Regarding claim 10, Raine teaches that the adapters are ligated (i.e., covalently linked) to the 3' and 5' ends of the ssDNA target using T4 DNA ligase ([0104]).
Regarding claim 15, Raine teaches that the ssNA hybridization regions of the first and second scaffold polynucleotides are random, i.e., each hybridization region is different than each other hybridization region ([0104]).
Regarding claim 17, Raine teaches that the ssNA hybridization region comprises a random sequence ([0104]).
Regarding claims 21 and 27, Raine teaches that a 3' amino modification is added to the 3'-terminal nucleotide of the random hexamer oligo (i.e., the first scaffold polynucleotide species) and that this modification is made in order to prevent self-ligation of the adapter (i.e., the modification is capable of blocking covalent linkage of the scaffold polynucleotide to another oligonucleotide [0104]).
Regarding claim 28, Raine teaches a final step (i.e., after the covalent linkage of the hybridization products) wherein the libraries are PCR amplified to produce DNA copies ([0086]). The steps of PCR inherently comprise the denaturing of the covalently linked hybridization products to generate single-stranded ligation products.
Regarding claim 39, Raine teaches that the nucleic acid composition comprises ssDNA ([0077], [0079] and [0104]).
8. Claims 2 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) in view Gu et al (United States Patent Application US20180230516, published 16 August 2018) as applied to claim 1 above, and further in view of Yijun et al (United States Patent Application No. US 20160177380, published 2016-06-23).
Regarding claims 2 and 7, the method of claim 1 is discussed fully above and incorporated here. Neither Raine nor Gu teach contacting the first oligonucleotide and/or the plurality of first scaffold polynucleotides with an agent comprising a phosphatase activity and dephosphorylating the first oligonucleotide and/or the first plurality of scaffold polynucleotide species.
However, Yijun teaches a first, second, third and fourth polynucleotide species wherein the first and second polynucleotide are hybridized to form an adapter and the third and fourth polynucleotide are hybridized to form a second adapter ([0003] and [0004]). Yijun teaches that any of the polynucleotide species are dephosphorylated ([0107]). Dephosphorylating the polynucleotide species inherently comprises contacting the species with an agent comprising a phosphatase activity. Yijun additionally teaches that the dephosphorylated linkers are ligated to phosphorylated target DNA, therefore the dephosphorylation inherently occurs prior to combining with the nucleic acid target (i.e., the nucleic acid composition of claim 1 [0107]).
It would have been obvious to one having ordinary skill in the art to have modified method of producing a nucleic acid library as taught by the combination of Raine and Gu to have incorporated an additional step of contacting the first or second oligonucleotide or the first or second scaffold polynucleotide with an agent comprising phosphatase activity prior to the combining step to arrive at the claimed invention with a reasonable expectation of success, as taught by Yijun ([0107]). The ordinary artisan would have been motivated to make this combination because Yijun teaches that dephosphorylation the linker (i.e., adapter) polynucleotides reduces their ability to form dimers instead of ligating to the appropriate target DNA ([0107]). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results, because the known techniques of the cited references predictably result in the treatment of polynucleotide molecules to reduce the occurrence of off target ligation.
9. Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018) as applied to claim 28 above, and further in view of Bibillo et al (International Patent Application No. WO 2019222523, with priority to 2018-05-16) and Rasmussen et al (International Patent Application No. WO 2019237032, with priority to 2018-06-07).
Regarding claim 29, the method of claim 28 is discussed fully above and incorporated here. Raine does not teach combining the single-stranded ligation products with a third oligonucleotide under conditions in which the third oligonucleotide is hybridized to a dimer of the first oligonucleotide and the second oligonucleotide and contact the dimer hybridization product with a cleavage reagent.
Bibillo teaches that adapter dimers are removed from a reaction mixture by hybridization to a complementary oligonucleotide linked to magnetic beads that are subsequently removed from the reaction ([0040]).
Rasmussen teaches that adapter dimer duplexes are designed such that any adapter dimers formed result in a known site in the adapter dimer that is digested by an appropriate restriction enzyme (i.e., a cleavage agent [0122]).
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the combination of Raine and Gu to incorporate an additional adapter removal step comprising the hybridization of a complementary single stranded oligonucleotide as taught by Bibillo, followed by contacting that hybridization product with a restriction enzyme as taught by Rasmussen to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make these combinations because it is well known in the art that even when steps are taken to mitigate the formation of adapter dimers some fraction will still form. Even a small amount of adapter dimer can be amplified in subsequent PCR steps, and the resulting product can “outcompete” the desired sequencing library in downstream sequencing steps. Adding an additional step to remove potential adapter dimers can mitigate this issue as is known in the art. In addition, it would have been obvious to one having ordinary skill in the art that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the removal of adapter dimers from sequencing library preparations.
10. Claims 40-42 are rejected under 35 U.S.C. 103 as being unpatentable over Raine et al (United States Patent Application No. US 20190194649, filed 2018-11-02) in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018) as applied to claim above, and further in view of Gansauge et al (Single-Stranded DNA library preparation form highly degraded DNA using T4 DNA ligase, Nucleic Acids Research, 45, 10, e79, 2017-01-24).
Regarding claim 40, Raine teaches the method of claim 1 as discussed fully above and incorporated here. Raine does not teach that the ssNA is not modified prior to the combining.
However, Gansauge teaches a similar method of single-stranded library preparation (FIG. 1, ssDNA2.0), wherein the target nucleic acids are only dephosphorylated and denature before library preparation begins (FIG. 1 caption). It is noted that the applicant’s specification states that adding a phosphate group to one or both ends of a nucleic acid, and denaturing a nucleic acid, are generally not considered modifying the nucleic acid (pg. 67 ¶ 2). For the purpose of examination, removing a phosphate group as described by Gansauge is being considered as an “equivalent” manipulation (i.e., not modifying) as the addition of a phosphate group as discussed by the applicant.
It would have been obvious to one having ordinary skill in the art to have substituted the bisulfite-treated ssDNA library taught by Raine in view of Gu with the degraded DNA library taught by Gansauge to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this combination because Gansauge teaches that single-stranded library preparation has significant advantages for certain sample types (pg. 1 column 2 ¶ 2). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the formation of single-stranded oligonucleotide libraries.
Regarding claim 41, Gansauge teaches that the native ends of the ssNA are present when the ssNA is combined with the first oligonucleotide and the plurality of first scaffold polynucleotide species (FIG. 1 and caption). It is noted that the applicant’s specification states that adding a phosphate group to one or both ends of a nucleic acid, and denaturing a nucleic acid, are generally not considered modifying the nucleic acid (pg. 67 ¶ 2). For the purpose of examination, removing a phosphate group as described by Gansauge is being considered as an “equivalent” manipulation as the addition of a phosphate group as discussed by the applicant.
Regarding claim 42, Gansauge teaches that the ssNA is from cell-free DNA (page 3 column 1 ¶ 3).
Double Patenting
11. 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.
12. Claims 1, 6, 8, 10, 15, 17, 21, 27-28 and 39 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 57, 59, 63 and 76 of U.S. Patent No. 11629345 in view of Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) and Gu et al (United States Patent Application US20180230516, published 16 August 2018). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the ligation of adapter duplexes to a composition of single-stranded nucleic acids (ssNAs).
Claim 59 of the issued patent teaches a method which has steps that include all of the limitations of instant claims 1 and 6, except the limitation wherein the ssNA is not combined with a single-stranded nucleic acid binding protein (SSB) prior to or during the combining and wherein the nucleic acid composition, the first oligonucleotide, the plurality of first scaffold polynucleotides, the second oligonucleotide, and the second plurality of scaffold polynucleotides are combined in a single reaction.
However, Raine teaches a method comprising the ligation of adapter duplexes to a composition of ssNAs in the absence of an SSB.
Gu teaches that the nucleic acid composition, the first oligonucleotide, the plurality of first scaffold polynucleotides, the second oligonucleotide, and the second plurality of scaffold polynucleotides are combined in a single reaction as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method disclosed in issued patent 11629345 to have removed the SSB from the ssNA as taught by Raine and to have combined the components in a single reaction as taught by Gu in order to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to eliminate the use of unnecessary reagents and reduce cleanup/purification steps related to the generation of the SSB-bound ssNA complex. One having ordinary skill in the art would have recognized that the known techniques of the cited reference could have been combined with the known techniques of the issued patent with predictable results, because these techniques predictably result in the formation of nucleic acid compositions comprising ssNAs ligated to adapters.
The limitations of instant claims 8, 10, 15, 17, 21, 27-28 and 39 are given in claims 55, 57, 59, 63 and 76 of the issued patent in view of Raines and Gu.
The issued claims do not teach a single claim that includes all of the limitations of claim 1+ in a single claim. However, it would have been prima facie obvious to one having ordinary skill in the art to have modified any one of the issued claims so as to have applied it to the ligation of duplex adapters to a composition of ssNAs. Since all the claims in the issued patent are directed toward ligating adapters to ssNA molecules, it would have been obvious to combine the methods of the issued claims to achieve the predictable outcome of preparing a sequencing library from ssNA.
Claims 2, 7 and 11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 57, 59, 63 and 76 of U.S. Patent No. 11629345 in view of Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) and Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Yijun et al (United States Patent Application No. US 20160177380, published 2016-06-23).
The teachings of each listed issued claim and additional references as they relate to claims 1 and 8 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of instant claims 2, 7 and 11.
However, Yijun teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified method of producing a nucleic acid library as taught by the issued patent in view of Raine to have incorporated an additional step of contacting the first or second oligonucleotide or the first or second scaffold polynucleotide with an agent comprising phosphatase activity prior to the combining step to arrive at the claimed invention with a reasonable expectation of success, as taught by Yijun ([0107]). The ordinary artisan would have been motivated to make this combination because Yijun teaches that dephosphorylation the linker (i.e., adapter) polynucleotides reduces their ability to form dimers instead of ligating to the appropriate target DNA ([0107]). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results, because the known techniques of the cited references predictably result in the treatment of polynucleotide molecules to reduce the occurrence of off target ligation.
Claim 29 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 57, 59, 63 and 76 of U.S. Patent No. 11629345 in view of Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) and Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Bibillo et al (International Patent Application No. WO 2019222523, with priority to 2018-05-16) and Rasmussen et al (International Patent Application No. WO 2019237032, with priority to 2018-06-07).
The teachings of each listed issued claim and additional references as they relate to claim 28 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of instant claim 29.
However, Bibillo and Rasmussen teach these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the issued patent in view of Raine to incorporate an additional adapter removal step comprising the hybridization of a complementary single stranded oligonucleotide as taught by Bibillo, followed by contacting that hybridization product with a restriction enzyme as taught by Rasmussen to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make these combinations because it is well known in the art that even when steps are taken to mitigate the formation of adapter dimers some fraction will still form. Even a small amount of adapter dimer can be amplified in subsequent PCR steps, and the resulting product can “outcompete” the desired sequencing library in downstream sequencing steps. Adding an additional step to remove potential adapter dimers can mitigate this issue as is known in the art. In addition, it would have been obvious to one having ordinary skill in the art that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the removal of adapter dimers from sequencing library preparations.
Claims 40-42 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 57, 59, 63 and 76 of U.S. Patent No. 11629345 in view of Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) and Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Gansauge et al (Single-Stranded DNA library preparation form highly degraded DNA using T4 DNA ligase, Nucleic Acids Research, 45, 10, e79, 2017-01-24).
The teachings of each listed issued claim and additional references as they relate to claim 1 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of instant claims 40-42.
However, Gansauge teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have substituted the bisulfite-treated ssDNA library taught by the issued patents in view of Raine with the degraded DNA library taught by Gansauge to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this combination because Gansauge teaches that single-stranded library preparation has significant advantages for certain sample types (pg. 1 column 2 ¶ 2). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the formation of single-stranded oligonucleotide libraries.
13. Claims 1, 6 and 40-42 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of copending Application No. 18/011,271 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the ligation of adapter duplexes to a composition of single-stranded nucleic acids (ssNAs).
Regarding instant claim 1, claim 1 and 5 of the copending application teaches the hybridization of duplex polynucleotide scaffolds with a nucleic acid composition comprising ssNAs, except the limitation wherein the nucleic acid composition, the first oligonucleotide, the plurality of first scaffold polynucleotides, the second oligonucleotide, and the second plurality of scaffold polynucleotides are combined in a single reaction.
Gu teaches that the nucleic acid composition, the first oligonucleotide, the plurality of first scaffold polynucleotides, the second oligonucleotide, and the second plurality of scaffold polynucleotides are combined in a single reaction as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to having modified the claims of copending application 18/011,271 with the one-pot reaction method taught by Gu to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to reduce sample loss due to purification or transfer between reaction vessels. In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited methods predictably result in the ligation of 5' and 3' splinted adapters to a single-stranded target nucleic acid.
The limitations of instant claims 6 and 40-42 are found in claims 5, 10 and 11 of the copending application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 8, 10, 15, 17, 21, 27-28 and 39 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 6 of copending Application No. 18/011,271 in view Gu et al (United States Patent Application US20180230516, published 16 August 2018) and further in view of Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the ligation of adapter duplexes to a composition of single-stranded nucleic acids (ssNAs).
The teachings of each listed copending claim and additional reference as they related to claims 1 and 6 have been given previously in this office action and are fully incorporated here.
None of these teach the limitations of claims 8-10, 15, 17, 21, 27-28 and 39.
However, Raine teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method disclosed in the copending application in view of Gu with the limitations taught by Raine in order to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have recognized that the known techniques of the cited reference could have been combined with the known techniques of the issued patent with predictable results, because these techniques predictably result in the formation of nucleic acid compositions comprising ssNAs ligated to adapters.
This is a provisional nonstatutory double patenting rejection.
Claims 2 and 7 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 6 of copending Application No. 18/011,271 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018) and Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02), and further in view of Yijun et al (United States Patent Application No. US 20160177380, published 2016-06-23).
The teachings of each listed copending claim and additional reference as they related to claims 1 and 6 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of claims 2 and 7.
However, Yijun teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified method of producing a nucleic acid library as taught by the copending application in view of Gu and Raine to have incorporated an additional step of contacting the first or second oligonucleotide or the first or second scaffold polynucleotide with an agent comprising phosphatase activity prior to the combining step to arrive at the claimed invention with a reasonable expectation of success, as taught by Yijun ([0107]). The ordinary artisan would have been motivated to make this combination because Yijun teaches that dephosphorylation the linker (i.e., adapter) polynucleotides reduces their ability to form dimers instead of ligating to the appropriate target DNA ([0107]). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results, because the known techniques of the cited references predictably result in the treatment of polynucleotide molecules to reduce the occurrence of off target ligation.
This is a provisional nonstatutory double patenting rejection.
Claim 29 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 6 of copending Application No. 18/011,271 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018) and Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02) and further in view of Bibillo et al (International Patent Application No. WO 2019222523, with priority to 2018-05-16) and Rasmussen et al (International Patent Application No. WO 2019237032, with priority to 2018-06-07).
The teachings of each listed issued claim and additional references as they relate to claim 28 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of instant claim 29.
However, Bibillo and Rasmussen teach these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the copending application in view of Gu and Raine to incorporate an additional adapter removal step comprising the hybridization of a complementary single stranded oligonucleotide as taught by Bibillo, followed by contacting that hybridization product with a restriction enzyme as taught by Rasmussen to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make these combinations because it is well known in the art that even when steps are taken to mitigate the formation of adapter dimers some fraction will still form. Even a small amount of adapter dimer can be amplified in subsequent PCR steps, and the resulting product can “outcompete” the desired sequencing library in downstream sequencing steps. Adding an additional step to remove potential adapter dimers can mitigate this issue as is known in the art. In addition, it would have been obvious to one having ordinary skill in the art that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the removal of adapter dimers from sequencing library preparations.
This is a provisional nonstatutory double patenting rejection.
14. Claims 1, 6 and 28 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 8 of copending Application No. 19/106,916 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018). Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are drawn to the ligation of adapter duplexes to a composition of single-stranded nucleic acids (ssNAs).
Regarding instant claims 1 and 6, claim 1 of the copending application teaches the all of the limitations of the instant claims except for the limitations where the components are combined in a single reaction.
Gu teaches that these components are combined in a single reaction as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to having modified the claims of copending application 18/011,271 with the one-pot reaction method taught by Gu to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to reduce sample loss due to purification or transfer between reaction vessels. In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited methods predictably result in the ligation of 5' and 3' splinted adapters to a single-stranded target nucleic acid.
The limitations of instant claim 28 are found in claim 8 of the copending application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 8, 10, 15, 17, 21, 27 and 39 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 8 of copending Application No. 19/106,916 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Raine et al (US Patent Application No. US 20190194649, filed 2018-11-02).
The teachings of each listed copending claim and additional reference as they related to claims 1 and 8 have been given previously in this office action and are fully incorporated here.
None of these copending claims teach the limitations of claims 8, 10, 15, 17, 21, 27 and 39.
However, Raine teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method disclosed in the copending application to have removed the SSB from the ssNA as taught by Raine in order to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification in order to eliminate the use of unnecessary reagents and reduce cleanup/purification steps related to the generation of the SSB-bound ssNA complex. One having ordinary skill in the art would have recognized that the known techniques of the cited reference could have been combined with the known techniques of the issued patent with predictable results, because these techniques predictably result in the formation of nucleic acid compositions comprising ssNAs ligated to adapters.
This is a provisional nonstatutory double patenting rejection.
Claims 2 and 7 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 6 of copending Application No. 19/106,916 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Yijun et al (United States Patent Application No. US 20160177380, published 2016-06-23).
The teachings of each listed copending claim and additional reference as they related to claims 1 and 6 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of claims 2 and 7.
However, Yijun teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified method of producing a nucleic acid library as taught by the copending claims in view of Gu to have incorporated an additional step of contacting the first or second oligonucleotide or the first or second scaffold polynucleotide with an agent comprising phosphatase activity prior to the combining step to arrive at the claimed invention with a reasonable expectation of success, as taught by Yijun ([0107]). The ordinary artisan would have been motivated to make this combination because Yijun teaches that dephosphorylation the linker (i.e., adapter) polynucleotides reduces their ability to form dimers instead of ligating to the appropriate target DNA ([0107]). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results, because the known techniques of the cited references predictably result in the treatment of polynucleotide molecules to reduce the occurrence of off target ligation.
This is a provisional nonstatutory double patenting rejection.
Claim 29 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 8 of copending Application No. 19/106,916 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Bibillo et al (International Patent Application No. WO 2019222523, with priority to 2018-05-16) and Rasmussen et al (International Patent Application No. WO 2019237032, with priority to 2018-06-07).
The teachings of each listed issued claim and additional references as they relate to claim 8 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of instant claim 29.
However, Bibillo and Rasmussen teach these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the method taught by the copending application to incorporate an additional adapter removal step comprising the hybridization of a complementary single stranded oligonucleotide as taught by Bibillo, followed by contacting that hybridization product with a restriction enzyme as taught by Rasmussen to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make these combinations because it is well known in the art that even when steps are taken to mitigate the formation of adapter dimers some fraction will still form. Even a small amount of adapter dimer can be amplified in subsequent PCR steps, and the resulting product can “outcompete” the desired sequencing library in downstream sequencing steps. Adding an additional step to remove potential adapter dimers can mitigate this issue as is known in the art. In addition, it would have been obvious to one having ordinary skill in the art that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the removal of adapter dimers from sequencing library preparations.
This is a provisional nonstatutory double patenting rejection.
Claims 40-42 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 19/106,916 in view of Gu et al (United States Patent Application US20180230516, published 16 August 2018), and further in view of Gansauge et al (Single-Stranded DNA library preparation form highly degraded DNA using T4 DNA ligase, Nucleic Acids Research, 45, 10, e79, 2017-01-24).
The teachings of each listed copending claim and additional reference as they relate to claim 1 have been given previously in this office action and are fully incorporated here.
None of these teach the additional limitations of instant claims 40-42.
However, Gansauge teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have substituted the generic library taught by the copending claims with the degraded DNA library taught by Gansauge to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this combination because Gansauge teaches that single-stranded library preparation has significant advantages for certain sample types (pg. 1 column 2 ¶ 2). In addition, the ordinary artisan would have known that the known techniques of the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the formation of single-stranded oligonucleotide libraries.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
15. Any issue not repeated in the Office Action was overcome by amendment to the claims.
Applicant’s arguments, see pg. 9-11 of applicant’s remarks, filed 19 December 2025, with respect to the rejections of claims 1-2, 7, 8, 10, 15, 17, 21, 27-29, and 30-42 under 35 U.S.C. § 102 and 103 have been fully considered and are not persuasive. Therefore, the rejection has been modified to address the amendments and these rejections are maintained.
Regarding applicant’s arguments related to the rejection of claim 1 under U.S.C. § 102, it is noted above and reiterated here that the broadest reasonable interpretation of amended claim 1’s recitation of “…or amplification products thereof” encompasses amplification products of an RNA target after the generation of cDNA. There is no specific method step claimed that would render this interpretation inoperable.
Regarding applicant’s arguments related to the rejection of claim 1 under U.S.C. § 103, applicant argues on pg. 10 and 11 of their remarks that the ordinary artisan would not have been motivated to combine Raine and Gu because Gu discloses undesired adapter:adapter byproduct, and Raine discloses a technique that uses low quantities of input DNA, and that these adapter byproducts risk being preferentially amplified during PCR in the library preparation step. These arguments are not found persuasive because Gu specifically teaches methods of reducing adapter dimer formation (e.g., by using a blocking oligonucleotide to reduce the amplification of adapter dimers; abstract) that enables them to perform these ligation steps in a single reaction vessel as described in detail in the rejection above. This method of using blocking oligonucleotides is known in the art for the use of RNA library preparation (as demonstrated by Gu) as well as in DNA library preparation (as evidenced by Jung, US20190093102; FIGs. 3 and 4, [0006], [0014] and [0015]).
Regarding the double patenting rejections, applicant argued that the NSDP rejections fail for the same reasons that the previous anticipation and obviousness rejections fail. These rejections have been updated in view of Gu as described fully above and incorporated here, therefore the applicant’s arguments are not persuasive. The response additionally requests that the examiner hold the provisional rejection in abeyance until otherwise allowable subject matter is identified in the instant application. However, a complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims or the filing of a terminal disclaimer in accordance with 37 CFR 1.321 in the pending application(s) with a reply to the Office Action (see MPEP § 1490 for a discussion of terminal disclaimers). Such a response is required even when the nonstatutory double patenting rejection is provisional. As filing a terminal disclaimer, or filing a showing that the claims subject to the rejection are patentably distinct from the reference application’s claims, is necessary for further consideration of the rejection of the claims, such a filing should not be held in abeyance. MPEP § 804(I)(b)(1). Therefore, for the reasons set forth above and those already of record, the provisional nonstatutory double patenting rejection is modified to address the amended claims, and maintained.
16. All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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.
Conclusion
17. Jung et al (United States Patent Application US20190093102, published 28 March 2019) is cited on the record as an evidentiary reference related to the use of blocking oligonucleotides in DNA library preparation methods as a means of reducing the impact of adapter-dimer byproducts on the final composition of a sequencing library.
18. No claims are allowed.
19. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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