DETAILED ACTION
Response to Amendment
The amendment filed 03/02/2026 is acknowledged. The amendment clarified aspects of claim 1 and 20 to specify that the amount of cDNA being synthesized over a set period is proportional to the maximum reverse transcriptase activity of the sample. Additionally, two new claims, claims 21 and 22, were added.
Regarding the Office Action mailed 12/12/2025, the rejection of claims 1-20 under 35 USC § 103 are maintained and reiterated below; applicant’s remarks will be addressed following the rejections.
Regarding the newly added claims 21 and 22, they are rejected under 35 USC § 103 as addressed below.
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.
Claim(s) 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Loughran (US 20190323095 A1) in view of Brooks (Brooks et al., Basics of Enzymatic Assays for HTS. In: Assay Guidance Manual, 2012).
Loughran teaches a method of detecting reverse transcriptase (RT) activity of a sample [p1 para0004] comprising:
Preparing a reaction mixture which includes mixing a sample, an RNA polymer, at least one primer, deoxy triphosphate nucleotides, a DNA polymerase, and reagents for reverse transcription [p1 para0004; p2 para0027];
Synthesizing complementary DNA (cDNA) using the RNA polymer as template [p1 para 0004];
Loughran uses MS2 phage RNA as the RNA template, but teaches that substitution by other available RNA templates is possible [p14 para[0175].
Loughran performs this reaction by first incubating at 42oC for up to 60 minutes to convert template RNA into cDNA[p15 para0179], followed by terminating the RT activity by incubating at 65oC for 20 minutes [p15 para0180].
Forming partitions after synthesizing, the partitions containing copies of the cDNA at partial occupancy and each partition including a portion of the reaction mixture [p1 para0004; p2 para0027; p13 para0172];
Loughran teaches the use of digital droplet PCR, which involves partitioning a sample so that each partition is read in a binary manner as to whether or not a target DNA is present, allowing for the absolute counting of the presence of individual DNA species [p13, para0170].
These partitions are individual droplets, each of which contain all the necessary components for reverse transcription, PCR amplification, and detection of PCR amplification [p2 para0027] via fluorescent probes [p9 para0133] specific to a portion of the RNA target [p16 para0197].
Amplifying a target representing the cDNA in the partitions [p14 para0175]; and
The droplets are thermocycled for 45 cycles [p3 para0037].
Collecting amplification data for the target from the partitions [p15 para0191].
Each droplet is individually flowed past a detector where the fluorescence of the probes can be read [p15 para0191].
Loughran fails to teach that cDNA is synthesized proportional to the maximum reverse transcriptase activity (maximum velocity) over a set synthesis period or the concentration at which the RNA template is provided to the reaction mixture.
However, Brooks describes enzymatic assay kinetics and elucidates how a reaction could be set up so that the entire synthesis period occurs at maximum velocity.
According to Brooks, initial velocity refers to the initial linear portion of an enzymatic reaction in which the velocity of the reaction does not change over time and the substrate is present in excess. Accordingly, this portion of the reaction, and how long it lasts for, is dependent on both enzyme concentration and substrate concentration. Brooks further teaches that once the initial velocity (i.e., linear) region of the enzymatic reaction is determined, all subsequent experiments should be conducted in this range. If experiments are performed outside of this range, then the reaction would be proceeding in a non-linear fashion and application of steady-state or rapid-equilibrium kinetics would be invalid. As a result, the substrate concentration, or conversely the concentration of enzyme in a sample, could not be reliably determined [p3-5]. As the initial velocity is equivalent to the maximum velocity in the linear region of the enzymatic reaction (per [0080] of the instant specification), any reaction occurring during this set period of time would be at maximum velocity.
Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filling date of the claimed invention to prescribe a set synthesis period for the method of Loughran by following the teachings of Brooks in order to ensure proportionality between cDNA synthesis and maximum reverse transcriptase activity so that calculation of initial enzyme concentration can be conducted.
Claim(s) 21-22 are rejected under 35 U.S.C. 103 as being unpatentable over Loughran (US 20190323095 A1) in view of Brooks (Brooks et al., Basics of Enzymatic Assays for HTS. In: Assay Guidance Manual, 2012).
Regarding claim 21, Loughran teaches that hydrolysis probes are present in each partition, composed of a fluorophore and a quencher [Figs. 2A-2C], and were designed to allow detection of an amplified product [p14 para0176]. Fluorescence occurs when the fluorophore is released from the quencher by the hydrolysis of the probe by a polymerase [p2-3 para0030].
Regarding claim 22, as previously discussed, Brooks teaches that linear progression curves for enzyme reactions can be achieved if a large excess of substrate over enzyme is used in the reaction, stating that typical ratios of substrate to enzyme are greater than 100 but can approach one million [p4, L1-4; p7, L3-4]. Per [0080] of the instant specification, the linear phase of the reverse transcription reaction is equivalent to the maximum velocity. Therefore, if appropriate concentrations of both substrate and enzyme are used as to keep the reaction of Loughran in the linear phase during a pre-determined synthesis period, as described by Brooks, then the reaction will be proceeding at its maximum velocity over the entirety of said synthesis period.
Furthermore, the concentrations of RNA polymer and RT primer used are clearly result effective parameters that a person having ordinary skill in the art would routinely optimize. It would have been customary for an artisan of ordinary skill to determine the optimal amount of each ingredient, i.e. the concentration of RNA polymer/RT primer, needed to achieve the desired results, i.e. maximum reaction velocity. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation," (In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)) See MPEP § 2144.05.
Response to Arguments
Applicant’s arguments filed 03/02/2026 have been fully considered but they are not persuasive.
Applicant argues that the amendments made to claims 1 and 20 specify that the cDNA synthesis remains proportional over the entirety of the synthesis period. Furthermore, applicant added two additional claims. Applicant asserts that these amendments and additions are not addressed by Loughran or Brooks, individually or combined.
As discussed in the above rejections of claims 21 and 22 and summarized below, the Examiner disagrees with this assertion.
Regarding the newly added claim 21, Loughran utilizes hydrolysis probes in each partition and thus anticipates this claim.
Regarding the amendments to claims 1 and 20 and the newly added claim 22, a skilled artisan would be motivated to prescribe a “set synthesis period” for which the enzymatic reaction would be proceeding in a linear fashion (i.e., at maximum velocity) so that initial enzyme concentration could be reliably determined. Furthermore, the concentrations of RNA polymer and RT primer used in order to achieve maximum velocity are clearly result effective parameters that a person having ordinary skill in the art would routinely optimize.
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.
/K.N.K./ Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/ Primary Examiner, Art Unit 1681