Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Applicant' s amendment filed 11/10/2025 is acknowledged. Claims 1, 6-7, 9, 12, 14-15, 17, and 20-21 have been amended. Claims 4-5, 11, 13, 16, and 18-19 have been cancelled. Claims 1-3, 6-10, 12, 14-15, 17, and 20-21 are pending in the instant application and the subject of this final office action.
All of the amendments and arguments have been reviewed and considered. Any rejections or objections not reiterated herein have been withdrawn in light of amendments to the claims or as discussed in this office action.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejection
Status of Prior Rejections/Objections:
The 112(b) rejections to claim(s) 4-7, 9, 12, 14-15, 17, and 20 is/are withdrawn in view of the amendments to or cancellation of the claims.
The prior art rejection(s) under 35 USC 103 directed to the following are withdrawn in view of the amendments
Claim(s) 1-2, 4-5, 8, 12, 15, and 17-18 as being unpatentable over Morishima in view of NEB
Claim 3 over Morishima in view of NEB and further in view of Nolan
Claim 6 over Morishima in view of NEB and further in view of Eyre
Claim 7 over Morishima in view of NEB and further in view of Bio-Rad
Claim 9 over Morishima in view of NEB and further in view of van der Vries
Claim 10 over Morishima in view of NEB and further in view of Giardina – 2009 and Giardina – 2007
Claim 14 over Morishima in view of NEB and further in view of Feher
New Ground(s) of Rejections
The new ground(s) of rejections were necessitated by applicant’s amendment of the claims.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1: The paragraph at the end of pg. 2 recites “desired amount of product in the whole genome application”; this should be “amplification”.
Appropriate correction is required.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP 2111.
Regarding claims 1 and 21, the term "maximum usable amount" lacks a limiting definition beyond its use in the specification and claims as an amount corresponding to "a defined concentration of nucleic acid" (pg. 11, lines 1-2; claim 1). The context given for the “maximum usable amount” is limited to the "whole genome amplification systems"; however, it is noted that this phrase does not appear in the specification. Neither does the specification define a specific context for a subsequent “use” under which context the artisan, for example, may be able to understand a “maximum”.
Therefore, the term “maximum usable amount” was interpreted broadly as a desired amount of a reference genome for said system in light of the use of the term “desired amount” elsewhere in the specification in the context of a quantitative reference [i.e., defined concentration] (e.g., pg. 23, line 8 and pg. 24, line 1), and with the further understanding that a “maximum usable amount” may depend on the artisan’s desired downstream application (e.g., forensics applications versus high fidelity requirement sequencing applications).
Regarding claim 6, the claim now recites “the signals of the amplification are classified as ‘amplification’ in an event of a statistically significant rise in the signals of the respective cycle or a respective time point”. Broadly interpreted, “a statistically significant rise in the signals” is under its broadest reasonable interpretation to mean that the values of the amplification exceed those of the respectively performed amplification cycles and/or defined time points under a recognized statistical hypothesis testing methodology as understood by an ordinarily skilled artisan, supported by pg. 17 and Fig. 2. The claim does not require any particular statistical test or significance threshold.
Regarding claim 14, as the specification is silent as to the definitions of the following terms, “multiplex PCR” was interpreted broadly to include any PCR reaction that amplifies (under typically optimized annealing conditions) at least two different DNA sequences simultaneously. “Singleplex PCR” was interpreted to include a PCR that amplifies (under typically optimized annealing conditions) one DNA sequence. “Nested PCR” was likewise interpreted broadly mean sequential amplification using different primer sets wherein the product(s) of the first amplification is/are used as a template for the second amplification and wherein the second set of primers amplifies one or more region(s) internal to the first set of primers.
Therefore, in the context of the claim, multiplex PCR was interpreted to include whole genome amplification techniques that comprise PCR. Nested PCR comprising a first multiplex PCR and at least one second singleplex PCR, likewise, was interpreted to include a whole genome amplification technique that comprises PCR or any other multiplexed PCR followed by PCR with one target per reaction.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3, 6-10, and 14-15 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new matter rejection.
Regarding claims 1-3, 6-10, and 14-15, claim 1 is amended to recite:
“identifying a first checkpoint when the detected signals indicate amplification of both the sample … and the reference genome …;
“after identifying of the first checkpoint, comparing intensity of the sample nucleic acids and a second comparative sample comprising a quantitative reference that contains a desired amount of product in the whole genome application [sic] and no amplification enzyme; and
“terminating the amplifying of the sample nucleic acids and reference nucleic acids in response to the intensity of the sample nucleic acids and the quantitative reference being equal.”
The claims have been limited to whole genome amplification and monitoring of comparative samples. The portions of the specification that refer to these embodiments recite intercalating dyes (pg. 10, para 2, spanning pg. 11, especially pg. 11, lines 14-23; specification 01/29/2021). The specification teaches against the use of fluorescent probes in whole genome amplifications: “In a classic whole genome amplification, fluorescent probes, as is customary in a real time-PCR, are not used; instead, the amplification product which forms is visualized and quantified by the use of specific dyes … [that] intercalate into double-stranded DNA …” (pg. 21, para 2, spanning pg. 22). The remainder of that same paragraph continues to discuss “charged fluorescent dye” and “the amount of double-stranded DNA” (pg. 23, lines 17 and 20).
The following paragraph is clear that a different embodiment is intended for use with [nucleic acid] probes: “This method can also be applied to a specific, targeted preamplification in which the amount of DNA that is synthesized in a preamplification is checked … specific primers are used instead of the whole genome. What can also be used here as probe instead of a dye which intercalates at double-stranded DNA is a specific fluorescently labeled probe which generates a fluorescent signal depending on synthesized DNA, for example a TaqMan probe with fluorophore and quencher.” (pg. 23, para 1).
Even should the references to whole genome amplification have not been limited to intercalating dyes and demarcated from targeted amplification, the only FRET probe specifically recited throughout the disclosure is a TaqMan or functionally similar “cleaved” probe (i.e., pg. 2, para 1; pg. 23, line 35; pg. 24, line 6), which is both well known in the art and explicitly taught (pg. 2, para 1; pg. 24, lines 2 and 8) to be cleaved during amplification [i.e., by the enzyme].
Claim 1 requires that 1) the detected signals indicate amplification for the identification of the first checkpoint, 2) the quantitative reference in the second comparative reference have no amplification enzyme and the monitoring begins after the amplification is identified, and 3) the intensity of the sample nucleic acids and the quantitative reference to be equal at some point. Even if such nucleic acids probes were contemplated for this embodiment, TaqMan probes, which require cleavage by amplification enzyme to meaningfully fluoresce, will only produce background levels of fluorescence in this scenario; it is not clear how such a no enzyme control would meet the limitation of being equal to the intensity of a sample undergoing amplification at any point subsequent to the first checkpoint.
Further, even if the artisan were to look to other nucleic acid probes (e.g., Molecular Beacons) beyond those clearly contemplated in the disclosure, such lack reduction to practice to demonstrate possession of the claimed scope of the invention. First, it would not have been clear given the teachings regarding targeted amplification where and how to locate nucleic acid probes for monitoring whole genome amplification. Dean (US 7,074,600 B2; granted 07/11/2006) teaches that amplification bias among loci within a genome may differ at least six orders of magnitude at different loci (col 43, para 5; Fig. 6), particularly for PCR-based WGA (e.g., instant claims 2 and 14). Second, Vet (Vet JA, et al. Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc Natl Acad Sci U S A. 1999 May 25;96(11):6394-9) teaches that the binding efficiency and therefore fluorescence that results from such nucleic acid probes as Molecular Beacons depends on the length of the target (pg. 6396, Results, para 1). In a system of whole genome amplification, which typically relies on random priming, the length of amplicons would be expected to have a high degree of variability. Similarly, no reduction to practice to address potential pitfalls (e.g., the number of probes, accounting for sequence bias in design, “jackpotting,” etc.) of such discrete markers of amplification for a whole genome was identified in the disclosure. Absent such reduction to practice and in light of Dean and Vet, the artisan would anticipate a high degree of variability in utilizing nucleic acid probes.
To satisfy the written description requirement, the specification must describe the invention in sufficient detail that one skilled in the art can reasonably conclude that the applicant had possession of the claimed invention at the time of filing.
The Applicant has only described intercalating dyes in the context of a no amplification enzyme control for a whole genome amplification system. By broadening the claims to any means of measuring of intensity, the scope now includes any means of producing intensity related to amplification (diverse FRET nucleic acid probes, intercalating dyes, SERS signals, etc.), despite only the species of intercalating dyes being described in this context. This broadening in the claim amendment adds new matter that was not disclosed in the specification as filed, and now changes the scope of the instant disclosure. Such broadly recited limitations recited in the present claim, which did not appear in the instant specification, in the PCT application, or the German application to which priority is claimed, introduce new concepts and do not comply with the written description requirements under 35 USC 112.
Claim Rejections - 35 USC § 112(b)
Claim 12 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 12, the claim recites “wherein: a second comparative sample without nucleic acid to be amplified and/or a third comparative sample having a defined amount of nucleic acid … [corresponding] to desired target amount of amplification product in the amplification of the whole genome, a reaction preparation of the third comparative sample contains no amplification enzyme …”
Claim 1 now recites “a second comparative sample comprising a quantitative reference that contains a desired amount of product in the whole genome application and no amplification enzyme”.
First, the relationship between “a second comparative sample” of claim 12 and the “second comparative sample” of claim 1 is unclear.
Second, the “second comparative sample” of claim 1 appears to be substantially the same as “a third comparative sample” of claim 12. It is not clear whether it is intended to have two different comparative samples lacking enzyme if the third comparative sample is chosen in claim 12 or if this is simply a renamed “second comparative sample” of claim 1.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 12 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Regarding claim 12, the claim recites “wherein: a second comparative sample without nucleic acid to be amplified and/or a third comparative sample having a defined amount of nucleic acid … [corresponding] to desired target amount of amplification product in the amplification of the whole genome, a reaction preparation of the third comparative sample contains no amplification enzyme …”
Claim 1 now recites “a second comparative sample comprising a quantitative reference that contains a desired amount of product in the whole genome application and no amplification enzyme”.
Under an interpretation where the “a second comparative sample” of claim 12 is replacing the “second comparative sample” of claim 1, claim 12 fails to comply with the requirements of 112(d) because it fails to include all limitations of the claim upon which it depends.
Response to Arguments
Applicant's arguments filed 11/10/2025 have been fully considered but they are not persuasive.
Applicant argues that, as claim 19 was previously indicated as allowable subject matter, claim 1 is also allowable without the intervening limitations of claim 17.
Claim 17 recites “the detected signal of the amplification is based on detection of light emitted by fluorescent dyes intercalated into double- stranded DNA”.
As has been discussed in the 112(a) new matter rejection above, the disclosure does not support such a broadening of the claims. Indeed, the parts of the disclosure concerned with whole genome amplification specifically recite intercalating dyes and set apart targeted amplification when FRET nucleic acid probes are discussed. Further, specifically named TaqMan/cleavable probes would not work in the quantitative reference, and no further integration to practice for whole genome amplification monitoring has been clearly contemplated. For this reason, the one of skill in the art would not have reasonably concluded that the applicant had possession of the full genus of any means of monitoring WGA, particularly no amplification enzyme controls. Thus, such a broadening represents new matter.
Prior Art
No prior art was found teaching the combination of method steps as recited in claims 12, 17, 20, or 21, which require terminating the amplifying of the sample nucleic acids and reference nucleic acids in response to the intensity of the sample nucleic acids and the quantitative reference being equal and that the detected signal of the amplification is based on a use of intercalating fluorescent dyes. The prior art made of record and not relied upon is considered pertinent to the applicant’s disclosure.
Nolan (Nolan T, Huggett J, Sanchez E, Good practice guide for the application of quantitative PCR (qPCR), LGC. 2013) teaches negative controls omitting enzyme, particularly reverse transcriptase, for the purpose of obtaining a representative estimation of the level of contamination in the analytical process and characterized positive controls positive samples that may be used to compare with test samples in post-amplification melt curve analysis or to assess the efficiency of the assay (pg. 16, A.2.4, Appropriate Controls). Nolan further teaches that signal carryover into neighboring sample wells may cause background fluorescence and that well-designed assays have low background compared to the amplified signal (A.6.1, Baseline correction, para 1). Nolan fails to teach or suggest a positive, no enzyme control sample [i.e., one containing a desired amount of end product] and its teachings further suggest that it would not have been obvious to one of ordinary skill in the art to utilize a sample with high initial fluorescent that could cause signal carryover into neighboring sample wells.
NEB (PicoPLEX WGA Kit [online]. NEB; 2014 [retrieved on 2025 Jan 16]. Retrieved from the Internet: https://www.neb.com/en-us/-/media/nebus/files/manuals/manuale2620.pdf) teaches that WGA-amplified samples should be compared to WGA-amplified control DNA rather than to un-amplified control DNA for the most accurate results (pg. 4, Amplification of Control DNA), thus one of ordinary skill would not have been motivated to include a quantitative reference sample that was not included in the amplification (i.e., lacked the amplification enzyme) as part of the automation.
Conclusion
Claims 20 and 21 are allowable. Claim 17 is objected to as depending from claim 1 and claim 12 stands rejected under 112(b) and 112(d).
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 Emma R Hoppe whose telephone number is (703)756-5550. The examiner can normally be reached Mon - Fri 11:00 am - 7:00 pm.
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/EMMA R HOPPE/Examiner, Art Unit 1683
/NANCY J LEITH/Primary Examiner, Art Unit 1636