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 .
Claim Rejections - 35 USC § 103
2. 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.
3. 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.
4. Claims 1, 6-8, 20, 21, 23-25, 27, 28, 30, 31, 36-37, 60, 61, 65, 67, 69, 70, and 81-84 are rejected under 35 U.S.C. 103 as being unpatentable over Francais et al (United States Patent Application No. US20200216891, published 09 July 2020) in view of Ju et al (United States Patent Application No. US20090263791, published 22 October 2009) and Silicycle (Application Note: Scavenging of Pd(dt-bpf)Cl2, published 2014). The rejection of claim 69 is evidenced by Golynskiy et al (United States Patent Application No. US20200131484, published 30 April 2020).
Regarding claims 1 and 20, Francais teaches a method for determining the sequence of a target polynucleotide ([0022]), comprising incorporating a nucleotide comprising a 3'-OH blocking group into a copy polynucleotide that is complementary to at least a portion of the target polynucleotide (i.e., a sequencing primer; [0023]), a solid support comprising at least 5,000,000 features/cm2 ([0210]) wherein multiple copies of a polynucleotide are present at each site and multiple target nucleic acids are manipulated simultaneously (i.e., multiplexing; [0209]). Francais teaches that all four nucleotide types are delivered to an array simultaneously with a DNA polymerase ([0200] and [0201]), that the solid support is imaged to determine the identity of incorporated nucleotides ([0201]), that the 3' blocking group of incorporated reversibly terminated nucleotides is cleaved by a palladium catalyst ([0121]) that is soluble in water (i.e., in aqueous solution) and the solution comprises tris(hydroxypropyl)phosphine ([0124]). Francais teaches washing unincorporated nucleotides and chemically removed byproducts from the copy polynucleotide strand, and that this sequential incorporation is repeated at least 50 – at least 250 times ([0026]).
Francais teaches that allyl protecting groups are used as caps for 3'-OH groups ([0008]), but does not specifically teach that these allyl protecting groups are chemically removed under the conditions disclosed. Francais teaches a palladium scavenger in the washing step ([0180]), but does not teach a palladium scavenger in the incorporation step or that the washing step has a Pd(II) scavenger and the incorporation step has a Pd(0) scavenger.
However, Francais teaches that the washing step comprising a palladium scavenger ([0180]). It would have been obvious to one having ordinary skill in the art, using the techniques taught in Francais, to have incorporated the palladium scavenger with the aqueous solution comprising the DNA polymerase in instant step (b) as well. The ordinary artisan would have been motivated to make this combination in order to reduce the risk of deblocking the 3'-OH during the coupling step and potentially double-coupling two bases during a single cycle.
Silicycle teaches that diamine compounds are effective scavengers of both Pd(0) and Pd(II) species (pg. 7, row 6).
Ju teaches a 3' allyl blocking group of the structure disclosed in in instant claim 1 (FIG. 1). Ju teaches that this allyl blocking group is removed by Pd-catalyzed (i.e., palladium) deallylation in aqueous buffer and “allows the re-initiation of the polymerase reaction,” i.e., exposes a 3'-OH group for further nucleotide incorporation ([0080]).
It would have been obvious to one having ordinary skill in the art to have simply substituted the generic palladium scavenger taught by Francais with a diamine scavenger as taught by Silicycle, and to have further substituted the 3' AOM protecting group taught by Francais with the 3' allyl protecting group taught by Ju to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this substitution because using a single dual-purpose scavenger would simplify buffer preparation and reduce the chance of applying the wrong scavenger at any particular step, and would have further recognized that the 3' allyl blocking group taught by Ju is removed under essentially the same conditions as those taught by Francais for the removal of the 3' AOM protecting group (aqueous Na2PdCl4 with P(PhSO3Na)3; Ju [0093] and Francais [0124]) and that one of these known elements could have been substituted for the other with predictable results.
Regarding claim 6, Francais teaches that the deblocking solution comprises ascorbate ([0182]).
Regarding claim 7, Francais teaches that the 3'-OH blocked nucleotide comprises a detectable label ([0134]) conjugated by a cleavable linker ([0140]).
Regarding claim 8, Francais teaches that the detectable label is a fluorescent dye ([0134]), and that the cleavable linker is either of the structures provided in instant claim 8 ([0150]), and that Z = -O-allyl ([0138]).
Regarding claim 21, Francais teaches sequencing on clustered arrays (i.e., distinct features on the array comprise multiple polynucleotide template molecules; [0216]). Francais teaches that the solid support comprises at least 5,000,000 features/cm2 ([0210]).
Regarding claim 23, Francais teaches that the purine bases are 7-deaza purines ([0136] and [0141]).
Regarding claims 24 and 25, Francais teaches that the T nucleotide has the disclosed structures ([0161] and [0264]) when the 3' AOM blocking group has been substituted with the 3'-O-allyl blocking group as taught by Ju, which has been discussed fully above and incorporated here.
Regarding claims 27 and 28, Francais teaches that the A nucleotide has the disclosed structures ([0161] and [0256]) when the 3' AOM blocking group has been substituted with the 3'-O-allyl blocking group as taught by Ju, which has been discussed fully above and is incorporated here.
Regarding claims 30 and 31, Francais teaches that the C nucleotide has the disclosed structure ([0161] and [0252]) when the 3' AOM blocking group has been substituted with the 3'-O-allyl blocking group as taught by Ju, which has been discussed fully above and is incorporated here.
Regarding claims 36 and 37, Francais teaches that that G nucleotide (i.e., at least one type of nucleotide) has the disclosed structure ([0262]) when the 3' AOM blocking group has been substituted with the 3'-O-allyl blocking group as taught by Ju, which has been discussed fully above and is incorporated here.
Regarding claim 60, Francais teaches that the sequencing cycles are repeated 50, 100 or 150 times ([0184]).
Regarding claims 61 and 65, Francais teaches that the phasing value is less than 0.25 or 0.18 after 150 or 50 cycles of sequencing ([0184]).
Regarding claim 67, Francais teaches that the deblocking solution comprises ethanolamine (i.e., a primary amine; [0244]).
Regarding claim 69, Francais teaches using DNA Pol 1901 (i.e., an altered archaeal family B polymerase comprising the modifications Leu408Ala, Tyr409Ala and Pro410Ile (i.e., the first, second and third amino acids of the 3-amino acid region 408-410 contain amino acids as required by instant claim 69; [0171] and [0278]). This rejection is evidenced by Golynskiy et al.
Regarding claim 70, Francais teaches sequencing kits comprising nucleotides and DNA polymerase ([0171]), and as discussed above and fully incorporated here, Francais in view of Silicycle teaches a Pd(0) scavenger and Francais in view of Ju teaches that these nucleotides comprise a 2’ deoxyribose moiety with a 3' allyl group attached to the 3' carbon atom as discussed fully above and incorporated here. Francais teaches that the DNA polymerase is Pol 1901 (i.e., an altered archaeal polymerase; [0171]). Francais further teaches that kits comprise additional components identified in methods and examples throughout the reference (e.g., the limitations of instant steps (b) and (c) as discussed fully above and incorporated here; [0165], and wherein the sequencing is performed over 150 cycles; [0184]).
Regarding claim 81, Francais teaches the tris(hydroxyalkyl)phosphine is tris(hydroxypropyl)phosphine (THPP; [0124]).
Regarding claim 82, Francais teaches that at least one type of the nucleotides comprises a nucleobase that is attached to a detectable label via a cleavable linker ([0134] and [0140]).
Regarding claim 83, Francais teaches that the detectable label is a fluorescent dye ([0134]), and that the cleavable linker is either of the structures provided in instant claim 8 ([0150]), and that Z = -O-allyl ([0138]).
Regarding claim 84, Francais teaches that each of the different nucleotides is labeled with a unique fluorophore (i.e., at least three of the nucleotides independently comprises a base that is attached to a detectable label; [0194]) and that the label is removed (i.e., attached via a cleavable linker; [0194]).
5. Claims 85 is rejected under 35 U.S.C. 103 as being unpatentable over Francais et al (United States Patent Application No. US20200216891, published 09 July 2020) in view of Ju et al (United States Patent Application No. US20090263791, published 22 October 2009) and Silicycle (Application Note: Scavenging of Pd(dt-bpf)Cl2, published 2014) as applied to claim 70 above, and further in view of Drmanac et al (United States Patent Application No. US 20180223358, published 09 August 2018).
Regarding claim 85, the method of claim 70 is discussed fully above and incorporated here.
Francais in view of Ju and Silicycle teaches at least two unlabeled nucleotides, wherein one of the unlabeled nucleotides comprises a functional moiety that allows it to become labeled ([0203]), however neither Francais, Ju nor Silicycle teaches that each of the four types of nucleotides are unlabeled and wherein the first and second unlabeled nucleotides each comprises a first and second functional moiety that is specifically bound by a first and second binding moiety of a first and second detectable label.
However, Drmanac teaches unlabeled reversible terminators that are incorporated during sequencing by synthesis and labeled after incorporation (abstract). Drmanac further teaches a set of unlabeled reversible terminators having a set of specific affinity reagents that bind to each reversible terminator to produce a labeled extension product (i.e., the set of affinity reagents comprises a first affinity reagent that binds to the first reversible terminator, a second affinity reagent that binds to a second reversible terminator, etc.; [0019]). Drmanac further teaches kits that comprises a plurality of such reversible terminators and a plurality of such labeling reagents ([0021]).
It would have been obvious to one having ordinary skill in the art to have simply replaced the cleavable-linker labeled reversible terminators taught by Francais in view of Ju with the unlabeled reversible terminator with their corresponding affinity reagents taught by Drmanac to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Drmanac specifically teaches that the use of unlabeled reversible terminators and their labeling with affinity reagents provides the advantage of not generating a chemical scar upon removal of the signal generating label after identification of the incorporated base that such scars reduces the efficiency of dNTP incorporation in standard sequencing by synthesis with labeled dNTPs ([0047]). 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 references predictably result in the sequencing by synthesis of nucleic acids.
Response to Arguments
6. Applicant's arguments filed 23 July 2026 have been fully considered but they are not persuasive.
It is noted on pg. 11 ¶¶ 2 and 3 of applicants remarks that applicant argues that the ordinary artisan “would have no reason to use the Pd(dt-bpf)Cl2 scavenger disclosed by Silicycle in the SBS reaction of Francais…” because Silicycle teaches the scavenging of a coupling reagent and Francais teaches the scavenging of a cleaving reagent (i.e., the prior art references teach scavengers for Pd species used in two different contexts). However, this is an overly narrow reading of the Silicycle reference and doesn’t address the section cited in the examiner’s rejection (pg. 7, row 6; the SiliaMetS Metal Scavengers portfolio). I.e., a list of scavengers that are not directly related to the coupling reaction case study described in the beginning of the reference, of which some scavenger species (such as row 6 indicated in the previous rejection) are known the efficiently scavenge Pd(0) and Pd(II) metal species.
Further, applicant additionally argues on pg. 11 ¶¶ 2 and 3 that Francais does not teach a Pd(0) scavenger in the incorporation mixture. However, in the previous Office Action (pg. 4 ¶ 4) this is addressed and a single-reference obviousness argument is made in which it is acknowledged that Francais teaches a Pd scavenger in one reaction step (corresponding to step (e) of the instant claims), and that it would have been obvious to one having ordinary skill in the art to have included the known scavenger taught by Francais in any of the other steps taught, to arrive at the instant invention with a reasonable expectation of success. This argument does not seem to be addressed in applicant’s remarks, only that Francais does not specifically teach a Pd(0) scavenger in the incorporation step.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
The rejections of claims 1 and 38 under 35 U.S.C. § 101 have been overcome by the cancellation of claim 38 in the instant application and the cancellation of claim 41 in the copending application 18393291. All other double patenting rejections applied previously have been overcome by the filing of appropriate terminal disclaimers.
7. 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.
Conclusion
8. No claims are allowed.
9. 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-T 0800 - 1630.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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