DETAILED ACTION
The amendment filed on 10/03/2025 has been entered.
Claims 1, 3-5, 7, and 8 were amended in the claim set filed on 10/03/2025.
Applicant’s election without traverse of Group I (claims 1-7) in the reply filed on 05/15/25 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 1-7 filed are currently under examination.
Response to the Arguments
Objections to the claims in the previously mailed non-final have been withdrawn in light of applicants claim amendments.
Applicant’s arguments regarding previous rejections of claims 1-7 under 35 U.S.C. § 112 have been fully considered and are persuasive. The 35 U.S.C. 112 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 5.
Applicant’s arguments regarding previous rejections of claims 1-7 under 35 U.S.C. 103 have been fully considered and are not persuasive. The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been maintained in light of applicants claim clarification, claim amendments and arguments on Pg. 5-6. As necessitated by amendment, revised rejections for claims 1-2 and 4-7 are made, as documented below, under the 35 U.S.C. 103 rejections in this office action on Pg. 3-7. A new ground of rejection is made for claim 3 under 35 U.S.C. 103 rejections in this office action on Pg. 8-9.
As necessitated by the filing of a terminal disclaimer over US 17/728,463, Applicant’s arguments regarding previous rejections of claims 1-7 under Nonstatutory Double Patenting have been fully considered and are persuasive. The Nonstatutory Double Patenting rejection documented in the previously mailed non-final have been withdrawn.
The rejections for claims 1-7 are documented below in this Final Office Action are necessitated by claim amendments filed on 10/03/2025.
Priority
This application is a 371 of PCT/US20/60333 filed on 11/13/2020 which claims benefit of 62/935,705 filed on 11/15/2019. Accordingly, the priority date of instant claims is determined to be 11/15/2019., the filing date of 62/935,705.
Claim Rejections - 35 USC § 103
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.
Claims 1-2 and 4-7 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Willey et al. (“Willey”; Patent App. Pub. No. WO 2014/082032 A1, May 30, 2014).
Willey discloses the Controlling for non-systematic error in an amplification-based next generation sequencing (NGS) library preparation comprises including of an internal amplification control (IAC) sharing identical priming sites to a native nucleic acid target template of interest in a NGS library preparation; and mimicking the kinetics of the native nucleic acid target in the amplification reaction, and controlling for sample-, platform-, experiment-, operator-and/or target-specific variation in amplification efficiency. (Abstract)
Regarding claim 1, Willey teaches a product comprising “internal amplification control (IAC)/competitive internal standards (IS) described herein may be assembled and provided in the form of kits” and “The IAC may be provided in… several known working concentrations” (Para. 238). Willey teaches a product comprising “Each nucleic acid target is similar to its respective internal standard, with the exception of one or more changes to the nucleic acid sequence. These differences between native target and internal standard are identifiable with sequencing, and can include … alteration to the ordering or composition of nucleotides used” (Para. 74). Willey teaches a product comprising “Each of the competitive IAC contained identical target-specific priming sites to their respective native nucleic acid template targets” (Para. 107) and “Internal standard… contains one or more base substitutions internal to the primer sites” (Para. 159).” Willey also teaches a product comprising “standardized mixtures comprising a competitive template for said first nucleic acid and a competitive template for a second nucleic acid … wherein said competitive templates are at known concentrations relative to each other … obtaining a first relationship…obtaining a second relationship … and comparing said first and said second relationships” (Para. 19) and “combined in a 1:1 stochiometric molar ratio” (Para. 154).
“The IS sequence, at each concentration, contains a nucleotide change at a different position along the sequence so that each IS sequence can be distinguished from the IS sequence at each other concentration” recited in instant claim 1 is interpreted as different IS sequences at different concentrations that are distinguishable, which is also broadly interpreted as “competitive templates at known concentration relative to each other”. “comparing said first and said second relationships” reads on at a known ratio relationship.
Thus, Willey teaches a kit for quantifying the amount of at least one nucleic acid of interest in a sample, comprising: spike-in internal standard (IS) reagents present as a complexity calibration ladder (CCL) that contains multiple synthetic internal standard (IS) sequences at different concentrations for a single endogenous target gene, wherein the IS sequence, at each concentration, contains a nucleotide change at a different position along the sequence so that each IS sequence is distinguishable from the IS sequence at each other concentration; and wherein the multiple internal standard (IS) sequences for the single endogenous target gene are mixed at different known concentrations relative to each other, and at a known ratio to IS for other targets.
The teachings of Willey are documented above in the rejection of claim 1 under 35 U.S.C. 103. Claims 2 and 6-7, depend on claim 1. Claims 4-5 depend on claim 2, which depends on claim 1.
Regarding claim 2, Willey teaches a product wherein “competitive IS corresponding to the endogenous targets” (Para. 153). Willey also teaches a product wherein “External RNA Control Consortium (ERCC)” (Para. 149) and “For the 28 competitive IS templates corresponding to ERCC targets, no such reference material exists for normalization” (Para. 155). Thus, Willey teaches a product wherein the spike-in IS reagents comprise one or more of: i) an endogenous complexity calibration ladder (ECCL) that includes synthetic internal standard competitors for at least one endogenous target gene; and ii) an alien complexity calibration ladder (ACCL) that includes synthetic internal standard competitors for at least one alien target gene.
Regarding claim 4, Willey teaches a product wherein “The kits may include … ERCC targets” (Para. 239). Thus, Willey teaches a product wherein the alien complexity calibration ladder (ACCL) comprises at least one of the External RNA Controls Consortium (ERCC) sequences.
Regarding claim 5, Willey teaches a product wherein “ERCC targets were synthesized” (Para. 151) and “Each ERCC target is at a different concentration” (Para. 160). Thus, Willey teaches a product wherein the endogenous complexity calibration ladder (ECCL) and/or the alien complexity calibration ladder (ACCL) comprises synthetic IS for the endogenous and/or alien target and includes IS sequences at different concentrations.
Regarding claim 6, Willey teaches a product wherein “The kits may also provide primers designed specifically to amplify the IS of 150 endogenous targets, the IS of 28 ERCC targets, and their corresponding native targets” (Para.240). The IS of 150 endogenous targets is interpreted as synthetic internal standards. Willey teaches a product wherein “internal amplification control (IAC)/competitive internal standards (IS) … provided in the form of kits” (Para.238). Willey teaches a product wherein “the kit provides the IAC and reagents necessary to perform a PCR, including Multiplex-PCR and next-generation sequencing (NGS).” (Para.238). Thus, Willey teaches a product further comprising reagents for measurement of expression and/or somatic mutations in multiple genes in a sample of cells, the kit including: a) PCR primers for each target gene; b) synthetic internal standard for each target gene; and c) reagents to prepare PCR products as a library for next generation sequencing, and/or oligonucleotides baits to capture IS and/or NT sequence fragments.
Regarding claim 7, Willey teaches a product wherein “a nucleic acid can comprise naturally occurring DNA, e.g., genomic DNA; RNA, e.g., mRNA, and/or can comprise a synthetic molecule, including but not limited to cDNA” and “can be, e.g., DNA, RNA, or hybrid DNA/RNA molecules” (Para. 62). Wiley teaches a product wherein “nucleic acid of interest" may be referred to as a "target" nucleic acid, and/or a "gene of interest," e.g., a gene being evaluated, may be referred to as a target gene” (Para. 61). Thus, Willey teaches a product wherein the nucleic acid of interest comprises one or more of: RNA to be measured, mRNA, DNA, cDNA, genomic DNA and variant alleles.
Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have developed a kit with spike-in internal standard reagents (endogenous and/or alien complexity ladder(s) at different concentrations) to be used in at least one of PCR, Multiplex-PCR and next-generation sequencing (NGS) as taught by Willey. One of ordinary skill in the art would have been motivated to do so in order to have a kit that is used for the standardization of nucleic acid sequencing. One of ordinary skill in the art would have had a reasonable expectation of success given that internal standards such as ACCL controls are known standards that have been developed as a standard amongst researchers to help measure reproducible lower limit sensitivity of quantified data and are commercially available.
Response to Arguments
Applicant' s arguments filed 10/03/2025 (Pg.6) with respect to claim 1-2 and 4-7 have been considered but are not persuasive. To clarify some instances argued in the response filed 10/03/2025 see responses to each argument made by Applicant below:
Applicants’ argument: “Willey does not teach or suggest a product where the internal standard (IS) sequence at each concentration contains a nucleotide change at a different position making each IS sequence distinguishable from others at different concentrations” (Pg. 13)
Response: Applicant's arguments filed 10/03/2025 have been fully considered but they are not persuasive. As necessitated by amendment, see revised rejection towards claim 1 under 35 U.S.C. 103. Applicant's arguments do not comply with 37 CFR 1.111(c) because they do not clearly point out the patentable novelty which he or she thinks the claims present in view of the state of the art disclosed by the references cited or the objections made. Further, they do not show how the amendments avoid such references or objections.
Applicants’ argument: “Willey describes a product and method wherein, for each target, the IS sequence has a set of distinguishing internal changes relative to the native sequence, but the same IS sequence is applied at various concentrations and differentiated by amount, not by unique positional variants that encode concentration. (See Willey, paragraphs [00135], [00238].) Willey does not teach or suggest the IS sequence, at each concentration, contains a nucleotide change at a different position along the sequence so that each IS sequence is distinguishable from the IS sequence at each other concentration.” (Pg. 13)
Response: Applicant's arguments filed 10/03/2025 have been fully considered but they are not persuasive. See response above towards claim 1.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Willey et al. (“Willey”; Patent App. Pub. No. WO 2014/082032 A1, May 30, 2014) in view of Jiang et al. (“Jiang”; (2011). Synthetic spike-in standards for RNA-seq experiments. Genome research, 21(9), 1543–1551.
This rejection is necessitated by claim amendments filed on 10/03/2025.
The teachings of Willey are documented above in the rejection of claims 1-2 and 4-7 under 35 U.S.C. 103. Claim 3 depends on claim 2, which depends on claim 1. Willey does not explicitly teach the limitations of claim 3.
Regarding claim 3, Willey teaches a product wherein “samples … were then combined with Ambion External RNA Controls Consortium (ERCC) Spike-In Control RNA Mixes” (Para. 144) and “Both the endogenous and ERCC target mixtures of competitive IS” (Para. 155). Of note, ERCC is specifically indicated as an example in the specification of the instant application (Para. 120, instant application). Thus, Willey teaches a product wherein the endogenous complexity calibration ladder (ECCL) is combined with an alien complexity calibration ladder (ACCL).
Although intrinsic to the design of ERRC Spike in controls, Willey does not explicitly teach that alien complexity calibration ladder is not competitive with the at least one endogenous target gene and is not affected by a sample's biological properties.
Regarding claim 3, Jiang et al. teaches a product wherein “Importantly, ERCC RNAs show minimal sequence homology with endogenous transcripts from sequenced eukaryotes. In RNA-seq experiments, this minimizes confounding alignment of ERCC reads to the target genome” (Pg. 1544, Col. 1, Results, Para. 2). Thus, Willey and Jiang teach a product wherein the endogenous complexity calibration ladder (ECCL) is combined with the alien complexity calibration ladder (ACCL), and wherein the synthetic internal standard competitors of the alien complexity calibration ladder (ACCL) are not competitive with the single endogenous target gene and is not affected by a sample's biological properties. A person of ordinary skill in the art would have had a reasonable expectation of success in providing a spike in control reagent that comprises an ERCC that is non-competitive since both claim elements were known before the effective filling date of the claimed invention. Doing so would eliminate interference with transcript discovery and quantification when using alien complexity calibration ladder such as ERRC spike-in controls in eukaryotic genomes.
Applicants’ argument: “Although Willey does describe that "[f]or the 28 competitive IS templates corresponding to ERCC targets, no such reference material exists for normalization" (see paragraph [0155]), this does not equate to teaching or suggesting an ACCL that is not competitive. Willey describes IS templates that are competitive and makes no mention of any that are not competitive.” (Pg. 13)
Response: Applicant's arguments filed 10/03/2025 have been fully considered but they are not persuasive, because the instant application recites “An additional option is to combine the "complexity calibration ladder" with an alien sequence ladder that is not competitive with endogenous targets and is not affected by a sample's biological properties. For example, one of the External RNA Controls Consortium (ERCC) sequences can be used as this alien ladder.” (Para. 122, instant application) Furthermore, ERCC spike-in controls were already known in the art as controls that were not competitive as evidenced by Jiang which has been added as prior art. See new grounds of rejections above for claim 3 made obvious over Willey and Jiang.
Conclusion of Response to Arguments
In view of the amendments, revised and new grounds of rejections, and responses to arguments are documented in this Final Office Action. No claims are in condition for allowance.
Conclusion
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 KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682