DETAILED ACTION
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 .
Claim Status
Claims 1-15 are currently pending and under exam herein.
Claims 1-15 are rejected.
Priority
The instant application filed June 16, 2022 is a 371 of PCT/EP2020/086752, filed December 17, 2020. The PCT application claims priority to German Patent Application No. DE 10 2019 220 020.6, filed December 18, 2019. At this point in examination, the effective filing date of the claims is December 18, 2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The Information Disclosure Statement filed 16 June 2022 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered.
Drawings
The Drawings filed on 06/16/2022 are accepted.
Specification
The abstract of the disclosure is objected to because improper text was included on the abstract sheet "Please add the following paragraph on a new page after claim 15 set forth on page 31 of the Applicant's specification" . A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 14 recites the limitation “The method as claimed in claim 1, wherein a computer program, is configured to perform and/or activate the method”, however it is unclear whether applicant is claiming a product (a computer program) or a method. The rejection may be overcome, for example, by amending the claim to recite a computer-readable medium comprising a computer program and instructions that, when execute, perform the method of claim 1.
Claims 15 recites the limitation "the method as claimed in claim 14, wherein the computer program is stored on a non-transitory machine-readable storage medium", however it is unclear whether applicant is claiming a product (a non-transitory machine-readable storage medium) or a method. The rejection may be overcome, for example, by amending the claim to recite a computer-readable medium comprising computer-executable instructions, that when executed, perform the method of claim 1.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 14-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim does not fall within at least one of the four categories of patent eligible subject matter because claim 15 is directed to a non-transitory machine-readable storage medium (a manufacture) yet depends from a method claim (claim 14), thereby rendering the statutory category of the claim unclear. This rejection may be overcome by amending the claim to depend from a claim of the same statutory category or by otherwise revising the claim to clarify its statutory category.
Furthermore, claim 14 recites a method wherein a computer program (product) is configured to perform and/or activate the method. Claim 14 may be amended, for, example, to recite a “computer-implemented method”.
Claims 1-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgment, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106:
Eligibility Step 1: Claims 1-14 are directed to a method (process) for determining a number of copies of a DNA sequence contained in a fluid and Claim 15 is directed to a non-transitory machine-readable storage medium (a manufacture, an article produced from materials). Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2 Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
setting a reaction condition for the fluid divided into the at least two compartments, in order in each case to allow a reaction in the at least two compartments and to obtain a reaction result for each (i.e., mental processes – one can think of the parameters to set a reaction condition);
and evaluating the signal, in order to determine the number of copies, based on a reaction-specific detection probability function, which indicates a probability of an amplification reaction occurring in a compartment of the at least two compartments in dependence on the number of copies initially present in the compartment of the at least two compartments (i.e., mathematical concepts – probability functions);
Dependent claims 2 further recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
The method as claimed in claim 1, wherein the evaluating the signal comprises: using a binomial distribution function for a statistical description of a distribution of the initially present copies among the at least two compartments for the determination of the number of copies (i.e., mathematical concepts – statistical model/probability calculation)
Therefore, claims 1 and 2 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Claim 2 does not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional element in independent claim 1 include:
determining a number of copies of a DNA sequence contained in a fluid;
dividing at least a predetermined part of the fluid into at least two compartments;
detecting a strength of a signal, which represents the reaction results of the reactions that have taken place in the at least two compartments;
The additional element in dependent claim 3 includes:
The method as claimed in claim1, wherein the detecting, the strength of the signal comprises: detecting the strength of an optical signal.
The additional element in dependent claim 4 includes:
The method as claimed in claim1, wherein, the evaluating, the signal comprises: investigating the fluid for multiple DNA sequences
The additional element in dependent claim 5 includes:
The method as claimed in claim1, wherein, the setting, the reaction condition comprises: introducing at least one additional reactant into the fluid.
The additional element in dependent claim 6 includes:
The method as claimed in claim1, wherein the setting the reaction condition comprises: setting the reaction condition at least partially only after the dividing.
The additional element in dependent claim 7 includes:
The method as claimed in claim1, wherein the evaluating the signal comprises: using an amplification reaction which has a detection limit which really is greater than 1 copy per reaction compartment.
The additional element in dependent claim 8 includes:
The method as claimed in claim1, wherein, the detecting, the strength of the signal comprises: recording spectral information of an optical signal.
The additional element in dependent claim 9 includes:
The method as claimed in claim1, further comprising: detecting the strength of the signal again at least one more time, in order to detect at least one further signal and to determine from the detected signals the reaction results of the reactions that have taken place in the at least two compartments by using the signals.
The additional element in dependent claim 10 includes:
The method as claimed in claim 9, further comprising: varying, between the detecting the strength of the signals, a time interval is wherein the evaluating the signals includes determining a cycle, a temperature, and/or a time interval at which a value of an optical signal, an increase in a value of the optical signal, and additionally or alternatively a rate of change in the value of the increase in the optical signal becomes a maximum.
The additional element in dependent claim 11 includes:
The method as claimed in claim1, further comprising: performing the method repeatedly; and at least partially performing at the same time the-a setting the reaction condition and the detecting the strength of the signal.
The additional element in dependent claim 12 includes:
The method as claimed in claim1, wherein the dividing at least the predetermined part of the fluid comprises: using a receiving unit with cavities.
The additional element in dependent claim 13 includes:
The method as claimed in claim1, wherein a controller is configured to perform and/or activate the method.
The additional element in dependent claim 14 includes:
The method as claimed in claim1, wherein a computer program is configured to perform and/or activate the method.
The additional element in dependent claim 15 includes:
The method as claimed in claim14, wherein the computer program is stored on a non-transitory machine-readable storage medium.
The additional elements of determining a number of copies of a DNA sequence contained in a fluid, dividing at least a predetermined part of the fluid into at least two compartments and detecting a strength of a signal, which represents the reaction results of the reactions that have taken place in the at least two compartments (claim 1); detecting the strength of an optical signal (claim 3); evaluating, the signal comprises: investigating the fluid for multiple DNA sequences (claim 4); setting, the reaction condition comprises: introducing at least one additional reactant into the fluid (claim 5); setting the reaction condition comprises: setting the reaction condition at least partially only after the dividing (claim 6); wherein the evaluating the signal comprises: using an amplification reaction which has a detection limit which really is greater than 1 copy per reaction compartment (claim 7); the detecting, the strength of the signal comprises: recording spectral information of an optical signal (claim 8); detecting the strength of the signal again at least one more time, in order to detect at least one further signal and to determine from the detected signals the reaction results of the reactions that have taken place in the at least two compartments by using the signals (claim 9); varying, between the detecting the strength of the signals, a time interval is wherein the evaluating the signals includes determining a cycle, a temperature, and/or a time interval at which a value of an optical signal, an increase in a value of the optical signal, and additionally or alternatively a rate of change in the value of the increase in the optical signal becomes a maximum (claim 10); performing the method repeatedly; and at least partially performing at the same time the-a setting the reaction condition and the detecting the strength of the signal (claim 11); the dividing at least the predetermined part of the fluid comprises: using a receiving unit with cavities (claim 12); a controller is configured to perform and/or activate the method (claim 13); a computer program is configured to perform and/or activate the method (claim 14) and the computer program is stored on a non-transitory machine-readable storage medium (claim 15) are insignificant extra-solution activities that are part of the data gathering process used in the recited judicial exceptions (see MPEP 2106.05(g)).
When all limitations in claims 1-15 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-15 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because the reasons noted below.
Dependent claim 2 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claim 1, and dependent claims 3-15 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at step Step 2A: Prong Two was re-evaluated at step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d). The additional elements of claims 1,3-6, 8 and 12 are conventional. Evidence for conventionality is shown by Quan et al. (“DPCR: A Technology Review. Sensors (Basel, Switzerland), vol. 18, no. 4, 20 Apr. 2018”). Quan et al. shows that a digital PCR method, in which a quantity of DNA copies in fluid is detected, divided in reaction compartments and used to calculate target concentration using probability function (Fig.3 -legend, pg.4) are conventional, the paper is a review and backs to 2018, showing the methods have been used for some time. Furthermore, in the specification, applicants disclose that their “invention is based on a method and a device for determining a number of copies of a DNA sequence contained in a fluid of the generic type of the independent claims. A computer program is also the subject of the present invention. The amplification of target-specific DNA base sequences plays an important role in particular in the molecular-diagnostic analysis of patient samples. Since the development of the so-called polymerase chain reaction (PCR), a large number of different detection variants and amplification reactions for nucleic acids have become established”, showing further conventionality. The additional elements of claims 7, 9-11 and 13-15 are conventional. Evidence for conventionality is shown by Valasek and Repa. (“The Power of Real-Time PCR.” Advances in Physiology Education, vol. 29, no. 3, Sept. 2005, pp. 151–159), which demonstrates a computer implemented PCR method that measures signals repeatedly, changes the reactions conditions such time and temperature, analyzes amplification to determine reaction results and perform data analysis using computer software, hardware and storage were conventional since the paper was published back in 2005, over 20 years ago.
Therefore, when taken alone, all additional elements in independent claim 1, and dependent claims 3-15 do not amount to significantly more than the above-identified judicial exceptions(s). Even when evaluated as combination, the additional elements fail to transform the exceptions (s) into patent-eligible application of that exception. Thus, claims 1-15 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-6, 8, and 12 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Quan et al. (“DPCR: A Technology Review. Sensors (Basel, Switzerland), vol. 18, no. 4, 20 Apr. 2018”).
Claim 1 is drawn to a method of determining how many copies of a DNA sequence are present in a liquid sample by dividing at least a portion of the liquid into two or more separate compartments, reaction conditions are then established for the sample in each compartment so that a reaction can occur in each one and produce an individual reaction result, a signal is detected that represents the reaction results of the reactions that have taken place in the compartments evaluating the signal to determine how many copies of DNA sequence, using a reaction specific probability model that describes the likelihood that an amplification reaction occurs in a compartment of the at least two compartments, based on the number of copies initially present in the compartment. In some embodiments, the signal is evaluated using binomial distribution function to describe how DNA copies were initially distributed among the compartments (claim 2); detecting the strength of an optical signal (claim 3); investigating the fluid for multiple DNA sequences (claim 4); introducing at least one additional reactant into the fluid (claim 5); setting the reaction condition at least partially only after the dividing (claim 6); detecting the strength of a signal by recording spectral information of an optical signal (claim 8); and dividing at least the predetermined part of the fluid comprises: using a receiving unit with cavities (claim 12).
With respect to the limitation of a method for determining a number of copies of a DNA sequence contained in a fluid, Quan et al. teach “(dPCR) is a novel method for the absolute quantification of target nucleic acids” (abstract, lines 1-2, pg. 1), in which PCR “is an in vitro technique that amplifies DNA, generating several millions of copies of a specific segment of DNA” (para3., lines 1-2, pg. 1) and further show that a DNA sequence contained in a fluid as seen in Figure 3 (pg.4).
With respect to the limitation of dividing at least a predetermined part of the fluid into at least two compartments, Quan et al. teach “the sample is divided into many independent partitions such that each contains either a few or no target sequences” (Fig.3 -legend, pg.4), meaning that a selected portion of the liquid sample is chosen in advance and then divided into multiple compartments.
With respect to the limitation of setting a reaction condition for the fluid divided into the at least two compartments, in order in each case to allow a reaction in the at least two compartments and to obtain a reaction result for each, Quan et al. teach “each partition acts as an individual PCR microreactor” (Fig.3, abstract, lines 3-4, pg. 1), meaning that each compartment is given the right conditions so a reaction can happen and produce its own result.
With respect to the limitation of detecting a strength of a signal, which represents the reaction results of the reactions that have taken place in the at least two compartments, Quan et al. teach “each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence” (Fig.3, abstract, lines 3-4, pg. 1), meaning each compartment produces a detectable signal after the reaction. Quan et al. further teach “dPCR collects fluorescence signals via end-point measurement” and “reduces quantification to the enumeration of a series of positive and negative outcomes” (para.1, lines 3-6, pg. 4), showing that the strength of the detected fluorescence signal represents the result of the reaction in the compartments, revealing whether amplification happened or not.
With respect to the limitation of evaluating the signal, in order to determine the number of copies, based on a reaction-specific detection probability function, which indicates a probability of an amplification reaction occurring in a compartment of the at least two compartments in dependence on the number of copies initially present in the compartment of the at least two compartments, Quan et al. teach “the proportion of amplification-positive partitions serves to calculate the concentration of the target sequence using Poisson’s statistics” (Fig.4 – legend, pg. 4), meaning dPCR uses the probability of obtaining a positive amplification result in the compartments, as determined from the detected signals, to determine the number of DNA copies that were present before the amplification.
With respect to claim 2, Quan et al. teach evaluating the signal using binomial distribution function to describe how DNA copies were initially distributed among the compartments, “To estimate the probability p of a partition to contain at least one target sequence, we should consider the case of the random distribution of m molecules into n partitions. This situation corresponds to a binomial process where the outcome of each drawing is either present or absent and the drawing is repeated m times” (para.3, lines 1-4, pg.5), meaning it uses a binomial distribution to model the initial distribution of DNA copies among the compartments.
With respect to claim 3, Quan et al. teach detecting the strength of an optical signal, “dPCR collects fluorescence signals via end-point measurement” and “reduces quantification to the enumeration of a series of positive and negative outcomes” (para.1, lines 3-6, pg. 4), fluorescence microscopy is an optical microscopy technique, therefore Quan et al. show that the strength of the detected optical signal (fluorescence) represents the result of the reaction in the compartments, revealing whether amplification happened or not.
With respect to claim 4, Quan et al. teach evaluating, the signal by investigating the fluid for multiple DNA sequences, “The co-amplification of two target sequences in the same partition produces a dual-colored signal” (para.4, lines 12-13, pg.7) further shows that a DNA sequence contained in a fluid as seen in Figure 3 (pg.4), meaning the fluid sample is examined for multiple DNA sequences.
With respect to claim 5, Quan et al. teach the reaction condition comprises: introducing at least one additional reactant into the fluid, “qPCR and dPCR use the same amplification reagents” (Fig.4, legend – line 3, pg. 4), meaning at least of one amplification reactant is added to the fluid so that the reaction can occur.
With respect to claim 6, Quan et al. teach setting the reaction condition at least partially only after the dividing (Fig.3 -legend, pg.4).
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With respect to claim 8, Quan et al. teach detecting the strength of a signal by recording spectral information of an optical signal, “The co-amplification of two target sequences in the same partition produces a dual-colored signal” (para.4, lines 12-13, pg.7). A “dual-colored signal” means the light has two different colors, which correspond to two wavelengths. To detect and differentiate these colors, the spectral information needs to be recorded.
With respect to claim 12, Quan et al. teach dividing at least the predetermined part of the fluid using a receiving unit with cavities, “In dPCR, the sample is first partitioned into many sub-volumes (in microwells, chambers or droplets)” (Fig.4, pg.4), and the sample is divided into many independent partitions such that each contains either a few or no target sequences” (Fig.3 -legend, pg.4), meaning that a selected portion of the liquid sample is chosen in advance and then divided into multiple compartments.
Claim 1 is rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Hindson et al. (“High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number.” Analytical Chemistry, vol. 83, no. 22, 15 Nov. 2011, pp. 8604–8610).
Claim 1 is drawn to a method of determining how many copies of a DNA sequence are present in a liquid sample by dividing at least a portion of the liquid into two or more separate compartments, reaction conditions are then established for the sample in each compartment so that a reaction can occur in each one and produce an individual reaction result, a signal is detected that represents the reaction results of the reactions that have taken place in the compartments evaluating the signal to determine how many copies of DNA sequence, using a reaction specific probability model that describes the likelihood that an amplification reaction occurs in a compartment of the at least two compartments, based on the number of copies initially present in the compartment.
With respect to the limitation of a method for determining a number of copies of a DNA sequence contained in a fluid, Hindson et al. teach that their method “enables the absolute quantitation of nucleic acids in a sample” (abstract, line 1, pg. 8604), mentions DNA specifically “High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number” (title, pg. 8604) and that the sample is a fluid “20 μL mixture of sample” (col.1, para.3, line 5, pg. 8605).
With respect to the limitation of dividing at least a predetermined part of the fluid into at least two compartments, Hindson et al. teach dividing at least a predetermined part of the fluid into at least two compartments, “divide a 20 μL mixture of sample and reagents into ∼20 000 monodisperse droplets (i.e., partitions)” (col.1, para.3, lines 5-6, pg. 8605).
With respect to the limitation of setting a reaction condition for the fluid divided into the at least two compartments, in order in each case to allow a reaction in the at least two compartments and to obtain a reaction result for each, Hindson et al. teach “into ∼20 000 monodisperse droplets (i.e., partitions). These droplets support PCR amplification of single template molecules using homogeneous assay chemistries and workflows” (col.1, para.3, lines 6-8, pg. 8605), meaning each droplet contains the materials and conditions needed for the reaction to occur. Hindson et al. further teach that the droplets are “thermal cycled to end-point” (Fig.1, col.1, para.4, line 14, pg. 8605), setting the temperature needed for PCR. Therefore, each droplet has its own reaction and produces its own result, such as whether amplification occurred or not.
With respect to the limitation of detecting a strength of a signal, which represents the reaction results of the reactions that have taken place in the at least two compartments, Hindson et al. teach that after the amplification reactions are finished, each droplet produces a signal that can be measured to determine what occurred during the reaction, “each droplet has an intrinsic fluorescence signal” (Fig.1, col.2, para.2, line 4, pg. 8605), meaning that every droplet generates a measurable signal. Hindson et al. further explain that the droplets are “aspirated and streamed toward the detector where, en route, the injection of a spacer fluid separates and aligns them for single-file simultaneous two-color detection” (Fig.1, results and discussion, lines 16-19, pg. 8605), showing that the fluorescence signal from which droplet is detected. Hindson et al. also state that the droplets are “droplets are assigned as positive or negative based on their fluorescence amplitude”, meaning that the brightness of the fluorescence signal shows how strong the signal is and is used to determine whether DNA amplification occurred in each droplet.
With respect to the limitation of evaluating the signal, in order to determine the number of copies, based on a reaction-specific detection probability function, which indicates a probability of an amplification reaction occurring in a compartment of the at least two compartments in dependence on the number of copies initially present in the compartment of the at least two compartments, Hindson et al. teach determining the number of DNA copies by analyzing the fraction of positive droplets using a probability based model, “The number of target DNA molecules present can be calculated from the fraction of positive end-point reactions using Poisson statistics” using the equation “λ = - ln(1- p)”, where “λ is the average number of target DNA molecules per replicate reaction and p is the fraction of positive end-point reactions” (eq1.,col.2, para.1, lines 4-10, pg.8604) meaning the Poisson calculation uses how often droplets turn positive to figure out how many DNA copies were in the droplets at the start.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claims 1-15 are rejected under 35 U.S.C. 103(a) as being unpatentable over Quan et al. (“DPCR: A Technology Review. Sensors (Basel, Switzerland), vol. 18, no. 4, 20 Apr. 2018”), and in view of Valasek and Repa. (“The Power of Real-Time PCR.” Advances in Physiology Education, vol. 29, no. 3, Sept. 2005, pp. 151–159).
The claims are drawn to a method of determining how many copies of a DNA sequence are present in a liquid sample by dividing at least a portion of the liquid into two or more separate compartments, reaction conditions are then established for the sample in each compartment so that a reaction can occur in each one and produce an individual reaction result, a signal is detected that represents the reaction results of the reactions that have taken place in the compartments evaluating the signal to determine how many copies of DNA sequence, using a reaction specific probability model that describes the likelihood that an amplification reaction occurs in a compartment of the at least two compartments, based on the number of copies initially present in the compartment. In some embodiments, the signal is evaluated using binomial distribution function to describe how DNA copies were initially distributed among the compartments (claim 2); detecting the strength of an optical signal (claim 3); investigating the fluid for multiple DNA sequences (claim 4); introducing at least one additional reactant into the fluid (claim 5); setting the reaction condition at least partially only after the dividing (claim 6); using amplification reaction which has a detection limit which really is greater than 1 copy per reaction compartment (claim 7), detecting the strength of a signal by recording spectral information of an optical signal (claim 8); the signal strength being checked at least one more time, to detect the signal again, and using the repeated signal readings to determine the reaction results that haven taken place in the at least two compartments (claim 9); evaluating the signals includes determining a cycle, a temperature, and/or a time interval at which a value of an optical signal, an increase in a value of the optical signal, and additionally or alternatively a rate of change in the value of the increase in the optical signal becomes a maximum (claim 10); the method being carried out multiple times, and during those times the reaction conditions are being set while the strength of the signal is being measured at the same time (claim 11); dividing at least the predetermined part of the fluid comprises: using a receiving unit with cavities (claim 12); a controller is configured to perform and/or activate the method (claim 13); a computer program is configured to perform and/or activate the method (claim 14), and the computer program is stored on a non-transitory machine-readable storage medium (claim 15).
With respect to the limitation of a method for determining a number of copies of a DNA sequence contained in a fluid, Quan et al. teach “(dPCR) is a novel method for the absolute quantification of target nucleic acids” (abstract, lines 1-2, pg. 1), in which PCR “is an in vitro technique that amplifies DNA, generating several millions of copies of a specific segment of DNA” (para3., lines 1-2, pg. 1) and further show that a DNA sequence contained in a fluid as seen in Figure 3 (pg.4).
With respect to the limitation of dividing at least a predetermined part of the fluid into at least two compartments, Quan et al. teach “the sample is divided into many independent partitions such that each contains either a few or no target sequences” (Fig.3 -legend, pg.4), meaning that a selected portion of the liquid sample is chosen in advance and then divided into multiple compartments.
With respect to the limitation of setting a reaction condition for the fluid divided into the at least two compartments, in order in each case to allow a reaction in the at least two compartments and to obtain a reaction result for each, Quan et al. teach “each partition acts as an individual PCR microreactor” (Fig.3, abstract, lines 3-4, pg. 1), meaning that each compartment is given the right conditions so a reaction can happen and produce its own result.
With respect to the limitation of detecting a strength of a signal, which represents the reaction results of the reactions that have taken place in the at least two compartments, Quan et al. teach “each partition acts as an individual PCR microreactor and partitions containing amplified target sequences are detected by fluorescence” (Fig.3, abstract, lines 3-4, pg. 1), meaning each compartment produces a detectable signal after the reaction. Quan et al. further teach “dPCR collects fluorescence signals via end-point measurement” and “reduces quantification to the enumeration of a series of positive and negative outcomes” (para.1, lines 3-6, pg. 4), showing that the strength of the detected fluorescence signal represents the result of the reaction in the compartments, revealing whether amplification happened or not.
With respect to the limitation of evaluating the signal, in order to determine the number of copies, based on a reaction-specific detection probability function, which indicates a probability of an amplification reaction occurring in a compartment of the at least two compartments in dependence on the number of copies initially present in the compartment of the at least two compartments, Quan et al. teach “the proportion of amplification-positive partitions serves to calculate the concentration of the target sequence using Poisson’s statistics” (Fig.4 – legend, pg. 4), meaning dPCR uses the probability of obtaining a positive amplification result in the compartments, as determined from the detected signals, to determine the number of DNA copies that were present before the amplification.
With respect to claim 2, Quan et al. teach evaluating the signal using binomial distribution function to describe how DNA copies were initially distributed among the compartments, “To estimate the probability p of a partition to contain at least one target sequence, we should consider the case of the random distribution of m molecules into n partitions. This situation corresponds to a binomial process where the outcome of each drawing is either present or absent and the drawing is repeated m times” (para.3, lines 1-4, pg.5), meaning it uses a binomial distribution to model the initial distribution of DNA copies among the compartments.
With respect to claim 3, Quan et al. teach detecting the strength of an optical signal, “dPCR collects fluorescence signals via end-point measurement” and “reduces quantification to the enumeration of a series of positive and negative outcomes” (para.1, lines 3-6, pg. 4), fluorescence microscopy is an optical microscopy technique, therefore Quan et al. show that the strength of the detected optical signal (fluorescence) represents the result of the reaction in the compartments, revealing whether amplification happened or not.
With respect to claim 4, Quan et al. teach evaluating, the signal by investigating the fluid for multiple DNA sequences, “The co-amplification of two target sequences in the same partition produces a dual-colored signal” (para.4, lines 12-13, pg.7) further shows that a DNA sequence contained in a fluid as seen in Figure 3 (pg.4), meaning the fluid sample is examined for multiple DNA sequences.
With respect to claim 5, Quan et al. teach the reaction condition comprises: introducing at least one additional reactant into the fluid, “qPCR and dPCR use the same amplification reagents” (Fig.4, legend – line 3, pg. 4), meaning at least of one amplification reactant is added to the fluid so that the reaction can occur.
With respect to claim 6, Quan et al. teach setting the reaction condition at least partially only after the dividing (Fig.3 -legend, pg.4).
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With respect to claim 8, Quan et al. teach detecting the strength of a signal by recording spectral information of an optical signal, “The co-amplification of two target sequences in the same partition produces a dual-colored signal” (para.4, lines 12-13, pg.7). A “dual-colored signal” means the light has two different colors, which correspond to two wavelengths. To detect and differentiate these colors, the spectral information needs to be recorded.
With respect to claim 12, Quan et al. teach dividing at least the predetermined part of the fluid using a receiving unit with cavities, “In dPCR, the sample is first partitioned into many sub-volumes (in microwells, chambers or droplets)” (Fig.4, pg.4), and the sample is divided into many independent partitions such that each contains either a few or no target sequences” (Fig.3 -legend, pg.4), meaning that a selected portion of the liquid sample is chosen in advance and then divided into multiple compartments.
Quan et al. teach a digital method absolute quantification of DNA. However, it does not teach directly the use of a computer (claims 13-15). They also do not teach using amplification reaction which has a detection limit which really is greater than 1 copy per reaction compartment; the signal strength being checked at least one more time, to detect the signal again, and using the repeated signal readings to determine the reaction results that haven taken place in the at least two compartments; evaluating the signals includes determining a cycle, a temperature, and/or a time interval at which a value of an optical signal, an increase in a value of the optical signal, and additionally or alternatively a rate of change in the value of the increase in the optical signal becomes a maximum; and the method being carried out multiple times, and during those times the reaction conditions are being set while the strength of the signal is being measured at the same time.
With respect to claim 7, Valasek and Repa. teach “Real-time PCR amplifies a specific target sequence in a sample then monitors the amplification progress using fluorescent technology. During amplification, how quickly the fluorescent signal reaches a threshold level correlates with the amount of original target sequence, thereby enabling quantification” (col.1, para.1, lines 3-8, pg. 152), meaning that the detection is threshold based instead of single molecule based, so it can only detect the signal when more than one copy is present in the at least one microwells (compartments).
With respect to claim 9, Valasek and Repa. teach ““Real-time PCR amplifies a specific target sequence in a sample then monitors the amplification progress using fluorescent technology” (col.1, para.1, lines 3-5, pg. 152), and “The amplification curve gives data regarding the kinetics of amplification of the target sequence”(col.1, para.2, lines 6-7, pg. 155), in which monitoring the amplification progress and amplification curve necessarily needs detecting the signal at least one more time, then the signals are used to determine the results of the reaction that happened in the at least one microwells (compartments), based on the signal data.
With respect to claim 10, Valasek and Repa. teach “The amplification curve gives data regarding the kinetics of amplification of the target sequence” (col.1, para.2, lines 6-7, pg. 155), “the final product can be further characterized by subjecting it to increasing temperatures to determine when the double-stranded product melts” (col.1, para.1, lines 9-11, pg. 152) and using “a thermocycler” (Fig.5, pg.154), meaning the signals are detected through many time based PCR cycles, involving adjusted temperature changes, and analyzed using melting curves and amplification, which are used to identify the cycle, the temperature or time where the signal is the maximum or changing.
With respect to claim 11, Valasek and Repa. teach that the PCR process is “repeated numerous times” (Fig.2, pg. 152), and Real-time PCR amplifies a specific target sequence in a sample then monitors the amplification progress using fluorescent technology” (col.1, para.1, lines 3-5, pg. 152) and the use of “a thermocycler” (Fig.5, pg.154), showing that the PCR method is done many times over many cycles, and the conditions of the reaction ( temperature cycling) are set by the thermocycler while the signal is measure during each cycle, so the set up for the reaction and the signal detection happen at the same time.
With respect to claims 13-15, Valasek and Repa. teach real time PCR methods which are computer implemented, “Real-time instrumentation certainly would not be complete without appropriate computer hardware and data-acquisition and analysis software. Software platforms try to simplify analysis of real-time PCR data by offering graphical output of assay results including amplification and dissociation (melting point) curves” (Fig.3, col.1, para.2, lines 1-6, pg.155), meaning that the real time PCR method is run and controlled by a computer, the software acquires data and analyzes it, then offers a graphical output, inherently requiring data to be stored in the computer during such operation.
It would have been obvious to one of ordinary skill in the art at the time the invention was made to modify the digital PCR method of Quan et al. with the computer implemented PCR method of Valasek and Repa., because the authors show that real time PCR has the “ability to quantify nucleic acids over an extraordinarily wide dynamic range (at least 5 log units). This is coupled to extreme sensitivity, allowing the detection of less than five copies (perhaps only one copy in some cases) of a target sequence, making it possible to analyze small samples like clinical biopsies” (col.1, para.3, lines 3-6, pg. 155). One would have had a reasonable expectation of success for making the combination because both references are related to PCR and Valasek and Repa., specifically teach that computer implemented real time PCR provides highly sensitive results even in small samples, therefore incorporating such technique would result in a much more sensitive quantification of DNA in a broader range of samples.
Conclusion
No claims are allowed.
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/A.S.E./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687