DETAILED ACTION
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office Action has been withdrawn pursuant to 37 CFR 1.114. Applicant’s submission filed 07/24/2026 has been entered.
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 .
Applicant’s Response
Applicant’s response, filed 07/24/2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Claims Status
Claims 1-3 and 5-21 are pending.
Claims 1-3 and 5-21 are examined.
Withdrawn Objections/Rejections
As stated in the Advisory Action mailed 08/13/2026, the rejection of claims 1-3 and 5-21 under 35 USC 112(b) is withdrawn. With respect to claims 1 and 18, Applicant clarifies that the claims do not recite an active training step, and thus training is not occurring within the confines of the claims. With respect to claim 16, the rejection is withdrawn in view of the amendments submitted.
Claim Rejections - 35 USC § 112
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.
Claim 16 is 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. The Specification provides support for fitting a clustering model, specifically a beta mixture model on alternative allele frequencies to model background sample and foreground contamination (paragraph [0049]), and other clustering models (paragraph [0050]), etc. However, the Specification does not provide support for training a probabilistic cluster model. This is a new rejection as necessitated by claim amendments.
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.
Claims 1-3, 5-21 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendments.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims are directed to processes, a non-transitory computer readable medium, and a system.
With respect to step (2A)(1): The claims are directed to abstract ideas of mental processes and mathematical concepts, and dependent claim 13 is directed to a law of nature.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claim 1:
identifying genetic variants from a molecularly sequenced sample from a subject
based on the identified genetic variants, identifying a set of alternative allele frequencies from the genetic variants that fall within a predetermined frequency range
generating a report identifying the determination of whether the sample is contaminated
Mathematical concepts recited in claim 1:
determining whether the sample is contaminated based on applying a probabilistic cluster model to the identified set of alternative allele frequencies, the probabilistic cluster model trained from molecular sequencing data representing contaminated and uncontaminated samples from subjects having the genetic variants
Mental processes recited in claim 16:
identifying genetic variants from the molecularly sequenced sample from the subject
based on the identified genetic variants, identifying a set of alternative allele frequencies from the genetic variants that fall within a predetermined frequency range and identifying a particular cancer and cancer treatment associated with the genetic variants
Mathematical concepts recited in claim 16:
determining whether the sample is contaminated by applying the probabilistic cluster model to the set of alternative allele frequencies within the predetermined frequency range
Mental processes recited in claim 18:
analyze the obtained molecular sequence to identify one or more genetic variants of the sample
based on the identified genetic variants, identify a set of alternative allele frequencies from the genetic variants and that fall within a predetermined frequency range
generate a report identifying the determination of whether the sample is contaminated
Mathematical concepts recited in claim 18:
determine whether the sample is contaminated based on applying a probabilistic cluster model to the identified set of alternative allele frequencies, the probabilistic cluster model trained from molecular sequencing data representing contaminated and uncontaminated samples from subjects having the genetic variants
Dependent claims 2, 3, 5-12, and 19-21 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claims 1 and 18, and as such, are further directed to abstract ideas. Dependent claim 13 recites a limitation that is directed to a law of nature. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas and judicial exceptions. The relevant recitations are:
Claim 2: “the frequency range is between 0 and 0.25”
Claim 3: “the frequency range is between 0 and about 0.01”
Claim 5: “wherein the probabilistic cluster model comprises a probabilistic mixture model”
Claim 6: “determining whether any of the alternative allele frequencies is an outlier, and removing any outliers from the set of alternative allele frequencies before the analysis of the alternative allele frequencies”
Claim 7: “determining whether any of the alternative allele frequencies is an outlier comprises a local outlier factor calculation”
Claim 8: “determining a level of contamination from the analysis of the alternative allele frequencies”
Claim 9: “determining the level of contamination comprises fitting the alternative allele frequencies to a mixture model”
Claim 10: “determining a confidence level around the level of contamination”
Claim 11: “determining a confidence level comprises bootstrapping the variants and the corresponding allele frequencies”
Claim 12: “identified genetic variants comprise particular genetic variants identifying a cancer and the therapeutic agent comprises a cancer drug selected […] to treat the cancer identified form the particular genetic variants”
Claim 13: “wherein the cancer drug performs better on a patient having a particular variant that on a patient without the particular variant”
Claim 19: “based on determining that the sample is not contaminated and based on the identified genetic variants, selecting and reporting the selection of a particular therapeutic agent designed to treat a condition or disease identified from the genetic variants”
Claim 20: “wherein the identified genetic variants comprise particular genetic variants associated with a cancer and the therapeutic agent comprises a cancer drug selected to treat the cancer associated with the particular genetic variants”
Claim 21: “based on determining that the sample is not contaminated and based on the identified genetic variants, selecting […] a particular therapeutic agent designed to treat a condition or disease identified from the genetic variants”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than using abstract ideas to determine if sample is contaminated based on an analysis of allele frequencies.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception 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 judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claim 1 recites the following additional elements that are not abstract ideas:
computer-implemented
Claim 16 recites the following additional elements that are not abstract ideas:
training a probabilistic cluster model programmed to determine whether a patient sample is contaminated, the probabilistic cluster model configured to use as input alternative allele frequences identified from molecular sequencing data of patient samples, wherein the training comprises the use of molecular sequencing data representing contaminated and uncontaminated
obtaining molecular sequencing data from a sample of a subject
based on determining that the sample is not contaminated, administering to the subject the particular cancer treatment associated with the genetic variants
Claim 18 recites the following additional elements that are not abstract ideas:
a molecular sequencer configured to generate a molecular sequence from the sample of a subject
one or more processors
obtain a molecular sequence of the sample of the subject generated by the molecular sequencer
The steps of sequencing and the step of training are directed to data gathering as it gathers the data on which the judicial exceptions are performed. The training step simply requires inputting data into a model. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). Furthermore, the elements of a processor and a computer-implemented method are directed to a generic computer. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). The step of administering “a particular therapeutic agent” is not a specific treatment and is akin to limitations requiring administering a suitable medication to a patient, which is not a particular enough administration of a treatment. Thus, this limitation does not recite a particular treatment step that integrates the judicial exceptions into a practical application (see MPEP 2106.04(d)(2)).
Dependent claims 14 and 15 are directed to further steps of data gathering as the limit the sequencing performed. Dependent claims 17 is directed to a non-transitory computer readable medium and thus elements of a generic computer. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application. Dependent claims 12 and 21 relate to generic treatments that do not integrate the judicial exceptions into a practical application (see MPEP 2106.04(d)(2)).
None of these dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that 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 provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d)(I), determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claim 1: The additional element of a computer-implemented method does not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 12: The additional element of the therapeutic agent comprises a cancer drug administered to the subject to treat the cancer identified form the particular genetic variants does not rise to the level of significantly more than the judicial exception. The prior art to Umbarger et al. (US 2014/0127688 A1, IDS reference) discloses that genetic testing is relied upon to a great extent for clinical pre-clinical diagnosis and the importance of detecting contamination so that a patient can be placed on the proper chemotherapeutic (paragraph [0048]). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 14: The additional element of the sample is sequenced to a mean sequencing depth of at least 1000x does not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(d) with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is a routine and conventional activity. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 15: The additional element of the sample is sequenced to a mean sequencing depth of at least 2000x does not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(d) with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is a routine and conventional activity. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 16: The additional elements of training a probabilistic cluster model, obtaining molecular sequencing data from a sample of a subject, and administering to the subject the particular cancer treatment associated with the genetic variants do not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(d) with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is a routine and conventional activity. The prior art Abelin et al. (US 2020/0096521 A1, filed February 2018) discloses that generating a prediction algorithm by training a machine is a well-known technique (paragraph [0219]). Furthermore, the prior art to Umbarger et al. discloses that genetic testing is relied upon to a great extent for clinical pre-clinical diagnosis and the importance of detecting contamination so that a patient can be placed on the proper chemotherapeutic (paragraph [0048]). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 17: The additional element of a computer product comprising a computer readable medium storing a plurality of instructions for controlling a computer system to perform an operation does not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 18: The additional elements of a molecular sequencer configured to generate a molecular sequence from the sample of a subject, one or more processors, and obtain a molecular sequence of the sample of the subject generated by the molecular sequencer do not rise to the level of significantly more than the judicial exception. As exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). Furthermore, with respect to sequencing, as exemplified in the MPEP at 2106.05(d) with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is a routine and conventional activity. The prior art Bao et al. (“Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing”, Sage Journals, published 2014) discloses a typical whole exome sequencing workflow comprising generating raw reads, preprocessing, alignment, variant calls, etc. (Figure 1) and thus a typical workflow requires a sequencer and a computer. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 21: The additional element of administering to the subject a particular therapeutic agent designed to treat a condition or disease identified from the genetic variants does not rise to the level of significantly more than the judicial exception. The prior art to Umbarger et al. discloses that genetic testing is relied upon to a great extent for clinical pre-clinical diagnosis and the importance of detecting contamination so that a patient can be placed on the proper chemotherapeutic (paragraph [0048]). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
In combination, the collection or generation of the data, acted upon by the judicial exception, fail to rise to the level of significantly more. The data gathering steps provide the data for the judicial exception. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
Response to Arguments
Applicant states “Claims 1-3 and 5-21 are directed to improving the necessarily computer-implemented and clearly practical technology of utilizing molecular sequences from patient samples to determine potential contamination of samples (e.g., claims 1, 16, and 18) and to further select and administer a particular therapy (e.g., cancer drug) based on a disease or condition (e.g., cancer) identified from variants in the molecular sequences (e.g., claims 12, 13, 16, and claims 19-21). There is no practical manner molecular sequences, and alternate allele frequencies from the samples (e.g., inherently containing millions of molecular bases) could be analyzed with mere “mental steps,” or that a probabilistic mixture model trained and applied as claimed could be implemented practically in the manner claimed to determine the contamination status of patient samples. Accordingly, the claims are not abstract. See, e.g., MPEP 2106.05(a), Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016), and DDR Holdings, LLC v. Hotels.com, 773 F.3d 1245 (Fed. Cir. 2014). The claims are not directed to the judicial exception of “mathematical concepts” either, but recite implementation of a machine learning model in order to achieve the concrete and non-abstract outcome of identifying contaminated samples with molecularly sequencing technology. Current law and the MPEP set forth that claimed technologies which may utilize mathematical concepts and raw data to produce concrete outcomes or results are not abstract. See MPEP 2106.04(a)(2)(I), “determining that the claims to a particular configuration of inertial sensors and a particular method of using the raw data from the sensors in order to more accurately calculate the position and orientation of an object on a moving platform did not merely recite “the abstract idea of using ‘mathematical equations for determining the relative position of a moving object to a moving reference frame’”), citing Thales Visionix, Inc. v. United States, 850 F.3d 1343, 1348-49, 121 USPQ2d 1898, 1902-03 (Fed. Cir. 2017). Accordingly, the transformation of raw sequencing data into concrete outcomes and recitation of certain calculations used to achieve the outcomes does not place the pending claims within the judicial exception of “mathematical equations.””
It is respectfully submitted that this is not persuasive. It is acknowledged that the molecular sequencer or obtaining sequences is not a mental process, within the 101 analysis it is interpreted as an additional element. Furthermore, as stated in the MPEP at 2106.04(a)(2).III.C, claims requiring a computer may still recite mental processes. Thus, the claims being computer-implemented does not prevent them from being directed to judicial exceptions. Furthermore, the claims do not require millions of molecular bases and thus the argument that the claims require too much data to perform the steps mentally is not persuasive. The steps of using the probabilistic model were not interpreted as a mental process but instead as a mathematical concept because it is an algorithm that is performing calculations using data. Claims 1 and 18 do not require any step of training this model, as stated by the Applicant in the response filed. Even though claim 16 does require a step of training the model, the training does not comprise more than the input of data. Furthermore, regarding the reference to Thales Visionix, Inc. v United States, the case differs because the use of the inertial sensors in Thales Visionix provided an unconventional arrangement, and the mathematical concepts were derived based on this unconventional arrangement of the sensors. This differs from the instant claims where math is applied to data in order to get a result and the mathematical concepts are not dependent on the data, and the data gathering is conventional. The instant claims 1 and 18 comprise reporting a result, no concrete outcome beyond reporting the result is performed and thus the essence of the invention is performing mental processes and applying mathematical algorithms to data in order to get a result. The instant claim 16 recites applying a generic treatment and do not recite enough particularity to recite a practical application (see MPEP 2106.04(d)(2). Therefore, the rejection under 35 USC 101 is maintained.
Applicant states “As set forth in Desjardins, examiners cannot simply dismiss “with a high level of generality” the subject matter eligibility of “any machine learning” as an “abstract” ineligible “algorithm,” as the FOA improperly does so in this case. “Categorically excluding AI innovations from patent protection in the United States jeopardizes America's leadership in this critical emerging technology. Yet, under the panel's reasoning, many AI innovations are potentially unpatentable-even if they are adequately described and nonobvious-because the panel essentially equated any machine learning with an unpatentable "algorithm" and the remaining additional elements as "generic computer components," without adequate explanation. Examiners and panels should not evaluate claims at such a high level of generality.” Desjardins at pg. 9. With a “high level of generality,” the FOA improperly dismisses all of the claimed limitations as “mental processes” (FOA pp. 5-7) despite the fact that one of ordinary skill in the art would recognize the combination of limitations as rooted in the technologies of machine learning as applied to molecular sequencing data for the “concrete outcome” of determining whether a patient’s sample has been contaminated with another sample. There is no manner of “mental process” that could sequence and process the inherently millions of DNA required to make and use the claimed invention.”
It is respectfully submitted that this is not persuasive. As stated above, not every claimed limitation was dismissed as a mental process. The 101 analysis does not claim that the molecular sequencing is a mental process. Instead, it generates the data on which the mental processes and mathematical concepts are performed. Furthermore, the claims do not require millions of DNA. The claims also do not elaborate on the machine learning model beyond applying a trained model and then determining whether a sample is contaminated. The machine learning model is not providing an improvement to the computer itself, it is not improving the efficiency of the computer or leading to an improvement in the amount of storage used, etc. The improvement and the outcome that Applicant is arguing are eligible are the judicial exceptions. Therefore, the rejection under 35 USC 101 is maintained.
Applicant states that “the FOA’s dismissal of limitations surrounding molecular sequencing as no more than a “general link to a technological environment” is inapt. FOA at 19. Molecular sequencing and improvements to the concrete application of machine learning to molecular sequencing to determine whether a patient sample is contaminated is at the root of the claimed invention, just as improving the processing of database functionality was at the root of eligible claims in Enfish. There can be no “untying” the combination of claimed features from the technological environments of molecular sequencing and machine learning, as the FOA erroneously suggests without basis.”
It is respectfully submitted that this is not persuasive. The additional elements of a molecular sequencer configured to generate a molecular sequence from the sample of a subject and obtaining a molecular sequence of the sample functions as a step to gather data on which the judicial exceptions are performed and is thus a data gathering step. The MPEP states that data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). Identifying genetic variants requires data in order to identify those variants, thus the additional elements are not serving as anything beyond providing the data on which the judicial exceptions are based. The MPEP gives an example that is considered mere data gathering wherein clinical tests are performed on individuals to obtain input for an equation. This is similar to the instant claims where a sequencing process is performed on a sample in order to obtain input for the analysis. The step of sequencing does not provide an improvement and does not implement any improvement that the judicial exceptions might be providing because it occurs before the judicial exceptions. Furthermore, sequencing is conventional, well-known, and routine (see MPEP at 2106.05(d) with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546). Therefore, the rejection under 35 USC 101 is maintained.
Furthermore, Applicant states that “Even if the present claims were considered to be directed to an “abstract idea,” the combination of recited features represent significantly more than a judicial exception and are integrated into a practical application. Claims directed to “abstract ideas” that are otherwise directed to improvements to particular technologies or technical fields represent significantly more than the judicial exception, are “integrated into a practical application,” and are patent eligible under § 101. MPEP §§ 2106.04(d)(1). The present claims are directed to improvements in diagnostic sequencing and sample contamination detection technologies that direct clinicians to better assess patients, and to properly select and execute treatment options. See, e.g., par. [0038] of the Specification as filed.”
It is respectfully submitted that this is not persuasive. It is the additional elements of the claims that are analyzed to determine whether the claims are integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). The additional element in claim 1 is a computer-implemented method. The additional elements in claim 18 comprise a molecular sequencer configured to generate a molecular sequence from the sample of a subject, one or more processors, and obtaining a molecular sequence of the sample of the subject generated by the molecular sequencer. As described above, the MPEP states that Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). Furthermore, the computer limitations represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)) and do not integrate the judicial exceptions into a practical application. With respect to claim 16, the step of training and obtaining sequences is considered data gathering as this supplies the data on which the judicial exceptions are performed. The step of administering treatments is not considered sufficient for a practical application because the treatment is not particular enough and instead the step recites a general step of administering a suitable treatment (see MPEP 2106.04(d)(2)). Furthermore, as discussed in Step 2B, these additional elements are conventional and thus the additional elements themselves do not provide an improvement. An improvement of the claims must be reflected within the additional elements of the claims by implementing or using the judicial exceptions in some manner beyond just generally linking the judicial exceptions to a technological field. Therefore, the rejection under 35 USC 101 is maintained.
Applicant further states that “the combination of elements of the present claims do not represent conventional or routine features, as would be required to establish with specific facts and evidence pursuant to Berkheimer v. HP, Inc., 881 F.3d 1360, 1368, 125 USPQ2d 1649, 1654 (Fed. Cir. 2018). The FOA does not even establish a lack of novelty or nonobviousness of the claimed features under 35 U.S.C. § 102 or 103, much less as being “conventional or routine.” Accordingly, for these additional reasons, the rejections of claims 1-18 under U.S.C. § 101 should be removed.”
It is respectfully submitted that this is not persuasive. It is the additional elements that are examined to determine if there is an inventive concept (MPEP 2106.05.A i-vi). as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). Furthermore, with respect to sequencing, as exemplified in the MPEP at 2106.05(d) with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is a routine and conventional activity. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. The claims not being rejected under 35 USC 102 or 103 does not mean that the additional elements are not conventional. Regarding claim 16, the prior art Abelin et al. discloses that generating a prediction algorithm by training a machine is a well-known technique (paragraph [0219]). Furthermore, the prior art to Umbarger et al. discloses that genetic testing is relied upon to a great extent for clinical pre-clinical diagnosis and the importance of detecting contamination so that a patient can be placed on the proper chemotherapeutic (paragraph [0048]). Furthermore, regarding claim 18, the combination of a molecular sequencer and a computing device with one or more processors is conventional and the foundation of many bioinformatics analysis pipelines is analyzing sequencing data using a computer. The prior art Bao et al. discloses a typical whole exome sequencing workflow comprising generating raw reads, preprocessing, alignment, variant calls, etc. (Figure 1) and thus a typical workflow requires a sequencer and a computer. Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
No claims are allowed.
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/E.A.S./Examiner, Art Unit 1686
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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