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 .
Status of the Application
2. Applicant’s response filed on April 20, 2026 has been entered.
Claims 1-5 are pending and under examination.
Response to Arguments
3. Applicant’s arguments filed on April 20, 2026 have been fully considered.
Rejections under 35 U.S.C. 103
Arguments:
Applicant’s arguments on pages 3-4 of the Remarks address both of the previously made rejections together. Here, Applicant first argues that the rejections should be withdrawn in view of the amendment to claim 1 requiring the blocker to target an undesired human blood or plasma RNA species (Remarks, pages 3-4). Applicant also argues that the ordinary artisan would not be motivated to remove the 3’ C3 spacer from the blocker of Wickersheim & Blumenstiel because that reference “indicate[s] that the presence of a 3’ C3 spacer may further contribute to ligation blocking” (Remarks, page 4).
Response:
In response, Applicant’s argument concerning the aforementioned amendment to independent claim 1 was persuasive. A new reference has been added to the rejections to address the new limitation in claim 1 concerning the blocker’s hybridization properties.
As well, Applicant’s argument regarding the 3’ C3 spacer in the blocker of Wickersheim & Blumenstiel was not persuasive because the ordinary artisan would have recognized that a 3’ dideoxy nucleotide, as proposed in the rejection based on the teachings of Wittwer, would serve the same purpose of blocking unwanted ligation. This is further supported by the prior art of Jiang et al. (WO 2016/058517 A1), which teaches that a 3’ C3 spacer or a 3’ dideoxy nucleotide can block unwanted ligation of a nucleic acid (see, e.g., page 19, last para.; see also page 1, third para.).
Claim Rejections - 35 USC § 103
4. 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.
5. 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.
6. Claims 1, 2, and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Wickersheim & Blumenstiel (BioTechniques 2013; 55: 269-272) in view of Chen et al. (Analytical and Bioanalytical Chemistry 2014; 406: 2477-2487) and also in view of Tsui et al. (Clinical Chemistry 2014; 60: 954-962; newly cited) and also in view of Wittwer et al. (US 2005/0233335 A1; newly cited) and further in view of Godfrey et al. (US 2006/0068433 A1).
The instant claims are drawn to a kit comprising a 3’ adapter, a 5’ adapter, and a single-stranded nucleic acid blocker that is complementary to an undesired RNA species.
Regarding claim 1, Wickersheim & Blumenstiel disclose a method that uses the following components: (i) a 3’ adapter, (ii) a 5’ adapter, and (iii) a single-stranded blocker nucleic acid that hybridizes to an undesired RNA species (i.e., 2S rRNA). See Figure 1 on page 270. Also, as can be seen in Figure 1, the blocker of Wickersheim & Blumenstiel does not form a unimolecular duplex under conditions suitable for hybridization of the blocker to the undesired RNA. Further regarding amended claim 1, the 3’ adapter of Wickersheim & Blumenstiel is blocked at the 3’ end with C3 spacer (Fig. 1).
Regarding claim 2, the 3’ adapter used by Wickersheim & Blumenstiel contains an rAPP at its 5’ end and also a 3’ blocking group (C3 spacer) (Fig. 1).
Regarding claim 5, the blocker used by Wickersheim & Blumenstiel contains a plurality of deoxyribonucleotides (Fig. 1).
Wickersheim & Blumenstiel do not teach providing the components of the method disclosed in Figure 1 in a kit as required by all of the instant claims. As well, Wickersheim & Blumenstiel do not teach or suggest that the blocker contains locked nucleic acid (LNA) as required by claim 1, from which claims 2-5 depend. Further, the 3’ adapter in Wickersheim & Blumenstiel contains a 3’ C3 spacer as the blocking group rather than the 3’ dideoxynucleotide required by amended claim 1.
Prior to the effective filing date of the invention, though, it would have been prima facie obvious for the ordinary artisan to modify the blocker of Wickersheim & Blumenstiel to contain at least one LNA (i.e., to form a blocker containing deoxyribonucleotides and at least one LNA as encompassed by claims 1 and 5). Chen provides motivation to do so by teaching that LNA offers the following benefits when provided in a blocker oligonucleotide designed to hybridize to an undesired nucleic acid present in a sample (see page 2484): (i) much greater binding affinity compared to DNA; (ii) better ability to discriminate between closely related target and nontarget sequences; (iii) ability to be designed to contain a modified 3’ phosphate, which prevents polymerase-mediated extension. The ordinary artisan would have recognized that these advantages of LNA would also to apply to the blocker of Wickersheim & Blumenstiel, and accordingly, would have been motivated to incorporate LNA into the Wickersheim & Blumenstiel to obtain the same benefits. The ordinary artisan also would have been motivated to not incorporate LNA at every position in the blocker of Wickersheim & Blumenstiel since Chen taught that an LNA/DNA chimera (e.g., as encompassed by the instant claim 5) can be used to “[t]o reduce costs…without decreasing sensitivity and specificity” (page 2484, col. 2). The ordinary artisan would have had a reasonable expectation of success in view of the guidance provided by Chen concerning LNA/DNA chimeras (pages 2478-2479).
It also would have been prima facie obvious to adapt the blocker suggested by Wickersheim & Blumenstiel in view of Chen such that it is complementary to an undesired RNA species present in a human blood or plasma sample. The blocker of Wickersheim & Blumenstiel is designed to target 2S rRNA, which is not present in humans, but the reference also teaches that it is generally desirable to remove high abundance RNA species that are not of interest when practicing high-throughput RNA sequencing (i.e., RNA-seq) (see the abstract; page 269, cols. 1-2; and page 271, last para.). And more specifically, Wickersheim & Blumenstiel expressly suggest adapting their disclosed strategy for rRNA depletion to other types of samples, stating, “Since rRNA excess is a general problem for RNA-seq, similar blocking strategies that limit adapter ligation and full-length cDNA synthesis may prove generally useful, limiting the need for magnetic beads and additional enzymatic steps” (page 271, last para.). Then, since Tsui also taught that it would be desirable to deplete rRNA from plasma samples prior to sequencing target RNA by a process comprising adapter ligation and cDNA synthesis (i.e., RNA-seq) (see, e.g., page 955, col. 2 and page 960), the ordinary artisan would have had further motivation to adapt the blocker suggested by Wickersheim & Blumenstiel in view of Chen to be complementary to undesired rRNA present in a human plasma sample. The ordinary artisan would have had a reasonable expectation of success since Wickersheim & Blumenstiel expressly suggested applying their blocking strategy to other systems and also since human rRNA sequences were known.
Further, it also would have been prima facie obvious to substitute the 3’ C3 spacer in the 3’ adapter of Wickersheim & Blumenstiel with a 3’ dideoxynucleotide. As discussed in MPEP 2144.06 and 2144.07, respectively, in the absence of unexpected results, it is prima facie obvious to substitute art-recognized equivalents known to be useful for the same purpose or to select a known material based on its suitability for the intended purpose. In this case, no evidence of unexpected results has been presented with respect to the use of a 3’ dideoxynucleotide on the 3’ adapter, and the teachings of Wittwer indicate that a 3’ dideoxynucleotide and a 3’ C3 spacer were each known to be useful for preventing unwanted polymerase-mediated extension of an oligonucleotide (see, e.g., para. 258). In other words, the teachings of Wittwer establish that a 3’ C3 spacer and 3’ dideoxynucleotide were art-recognized equivalents known to be useful for the same purpose of blocking unwanted polymerase-mediated extension of an oligonucleotide. The teachings of Wittwer, in combination with the lack of evidence of unexpected results concerning the presence of a 3’ dideoxynucleotide in the 3’ adapter, is sufficient to establish a prima facie case of obviousness per MPEP 2144.06 and 2144.07.
Lastly, it would have been prima facie obvious to provide (i) the blocker suggested by Wickersheim & Blumenstiel in view of Chen and Tsui, (ii) the 3’ adapter suggested by Wickersheim & Blumenstiel in view of Wittwer, and (iii) the other reagents used by Wickersheim & Blumenstiel in a kit. Since Godfrey taught that kits can be “particularly useful” for commercializing nucleic acid detection methods that make use of reagents that include oligonucleotides and DNA polymerases (para. [0112]), the ordinary artisan would have recognized that the library preparation method disclosed in Figure 1 of Wickersheim & Blumenstiel, which comprises adapter ligation, reverse transcription, and amplification (i.e., the use of oligonucleotides and polymerases) could also be commercialized by providing the reagents used to practice the methods (i.e., the blocker nucleic acid suggested by Wickersheim & Blumenstiel in view of Chen and Tsui, the 5’ adapter used by Wickersheim & Blumenstiel, and the 3’ adapter suggested by Wickersheim & Blumenstiel in view of Wittwer) in a kit. Accordingly, the ordinary artisan would have been motivated to provide such a kit to obtain the ability to commercialize the suggested library preparation method. The ordinary artisan would have had a reasonable expectation of success in view of the guidance provided by Godfrey in paras. [0112]-[0115].
Thus, the kits of claims 1, 2, and 5 are prima facie obvious.
7. Claims 3 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Wickersheim & Blumenstiel (BioTechniques 2013; 55: 269-272) in view of Chen et al. (Analytical and Bioanalytical Chemistry 2014; 406: 2477-2487) and also in view of Tsui et al. (Clinical Chemistry 2014; 60: 954-962; newly cited) and also in view of Wittwer et al. (US 2005/0233335 A1; newly cited) and further in view of Godfrey et al. (US 2006/0068433 A1) and further in view of Vigneault et al. (Current Protocols in Human Genetics 2012; Chapter 11: pp. 11.12.1 – 11.12.10).
As discussed above, the teachings of Wickersheim & Blumenstiel in view of Chen, Tsui, and Wittwer and further in view of Godfrey render obvious the kits of claims 1, 2, and 5.
Regarding claims 3 and 4, the method disclosed in Figure 1 of Wickersheim & Blumenstiel comprises ligation, but the reference, including the supplemental information, fails to specify that a ligase was used. Godfrey, Chen, Tsui, and Wittwer do not remedy this deficiency.
Wickersheim & Blumenstiel do teach, though, at pages 269-270 that the method disclosed in Figure 1 is based on the protocol disclosed in the Vigneault reference cited above. The Vigneault reference teaches the use of truncated T4 RNA ligase 2 for ligation of a 3’ adapter that contains a 5’ rAPP and the use of T4 RNA ligase 1 for ligation of a 5’ adapter. See pages 11.12.3 and 11.12.5 of Vigneault.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for the ordinary artisan to further include the two ligases disclosed in Vigneault in the kit suggested by the teachings of Wickersheim & Blumenstiel in view of Chen, Wittwer, and Tsui and further in view of Godfrey. As noted above, the method disclosed in Wickersheim & Blumenstiel includes ligation of a 5’ and 3’ adapter, but the reagent(s) used for the ligation reactions are not disclosed. The protocol from which the method of Wickersheim & Blumenstiel was adapted, though, uses truncated T4 RNA ligase 2 and T4 RNA ligase 1 for adapter ligation (pages 11.12.3 and 11.12.5). Therefore, when seeking to commercialize the method disclosed in Wickersheim & Blumenstiel by providing reagents for performing the method in a kit, the ordinary artisan would have been motivated to further include ligases suitable for use in the method, recognizing that doing so would result in a more useful kit. Thus, the kits of claims 3 and 4 are prima facie obvious.
Conclusion
8. No claims are currently allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
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