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 .
Introductory Remarks
In response to communications filed on 11 December 2025, claims 1, 3-4, 6-20, and 29-30 are amended per Applicant's request. Claims 5, 21-28, and 31-56 are cancelled. No claims were withdrawn. No new claims were added. Therefore, claims 1-4, 6-20, and 29-30 are presently pending in the application, of which claims 1, 29, and 30 are presented in independent form.
The previously raised objections to claims 8-10 have been withdrawn in view of the amendments to the claims.
The previously raised 112(b), indefiniteness rejection of the pending claims is withdrawn in view of the amendments to the claims.
The previously raised 112(d) rejection of claims 3 and 5 are withdrawn in view of the amendments to claim 3, and the cancellation of claim 5.
The previously raised 101 rejection of the pending claims is maintained.
The previously raised 103 rejection of the pending claims is maintained.
Response to Arguments
Applicant’s arguments filed 11 December 2025 with respect to the 112 rejection of the pending claims (see Remarks, p. 9) have been fully considered. The amendments overcome the previously raised rejection, and the rejection has been accordingly withdrawn.
Applicant’s arguments filed 11 December 2025 with respect to the rejection of the claims under 35 U.S.C. 101 (see Remarks, p. 9-10) have been fully considered but are not persuasive.
Applicant argues that, even if the claims recited a judicial exception, the claims as a whole integrates the judicial exception into a practical application via improving the functioning of a computer, another technology, or technical field (see Remarks, p. 10). Applicant recites the purported improvement, e.g., “reduc[ing] the number of computationally expensive processes performed by various sequencing technologies by not analyzing the removed data” (see Remarks, p. 10) (emphasis added).
However, Applicant’s characterization of patent eligibility is incorrect. The mere recitation that there is some improvement which results from performing the abstract idea, does not render claims patent eligible. Rather, the question is whether there is a concrete embodiment or concrete solution, to the identified problem.
Applicant claims a solution by processing only the data that passes quality checks. However, notably, this is not what the independent claims recite. The independent claims are focused on the validation. From the independent claims, it is clear that the problem to be solved is in how the quality checks are performed, such that the information is reduced.
Indeed, in the same paragraph cited by Applicant to list the purported improvement, the Specification at [0090] states “Employing such quality control techniques also provides an improvement to sequencing technology and computer technology”. This indicates that it is the use of specific quality control techniques that leads to the improvement. However, the claims themselves do not state which quality control techniques are specifically utilized to effect such improvements. In other words, as stated by the Specification, certain quality control techniques are what leads to the improvement, not that the results of the abstract idea are what leads to the improvement.
Therefore, as there is no specificity within the claims as to what those quality control techniques are, there is a lack of a concrete solution to that particular problem, i.e., improvement to the underlying technology.
Even when taking in combination the elements, i.e., as a whole, the additional elements do not amount to significantly more. The additional elements do not further limit the claims to a particular manner by which the essential focus of the claims—namely, quality checking—is performed, but rather only add insignificant field-of-use limitations and extra-solution activities.
By not stating how the quality check is performed, the quality check itself would become little more than making an observation, evaluation, and/or judgment (which falls under “Mental Processes” grouping of abstract ideas), even possibly mere data filtering (which falls under “Certain methods of organizing human activity” grouping of abstract ideas), when claimed in the context of being applied to downstream processing, i.e., filtering out data not meeting a particular quality threshold, and processing only those data meeting the particular quality threshold (which, in combination is a mental task or process for making such comparisons/determinations/observations/judgments, as well as insignificant field-of-use limitations, describing the context rather than a particular manner of achieving the result).
Thus, for at least the aforementioned reasons and those set forth in the 101 rejection below, the 101 rejection has been maintained.
Applicant’s arguments filed 11 December 2025 with respect to the rejection of the claims under 35 U.S.C. 103 (see Remarks, p. 11-12) have been fully considered but are not persuasive.
Applicant argues that “Walk simply does not describe sequencing of RNA or DNA molecules and then using the resulting sequencing data for any purpose” (see Remarks, p. 11-12) (emphasis added).
Applicant has mischaracterized the claim by using the terminology “sequencing of” the data.
However, the claim states “obtaining nucleic acid data comprising: sequence data indicating a nucleotide sequence…”. “Obtaining” and “sequencing” are not equivalents, as “sequencing” is a specific process of analyzing samples to generate data, whereas “obtaining” means, for example, that data (comprising the already-sequenced data) is provided.
This interpretation is consistent with the Specification, which states in, e.g., [0010], “the sequence data may include [various data]…obtained from a sequencing platform and/or comprising data derived from data obtained from a sequencing platform”. As seen, the data itself is not being sequenced by the claimed method, but rather data that has already been sequenced is part of the “obtaining step”.
As a result, the claim states “obtaining” the nucleic acid data, not “sequencing” the data as asserted by Applicant. This nucleic acid data, which comprises the sequencing data (i.e., already-processed / already-sequenced data), as well as asserted information, is obtained. The nucleic acid data is validated by processing the sequence data.
Furthermore, Applicant’s argument that Walk does not “us[e] the resulting sequencing data for any purpose”. This is incorrect, as Walk discloses utilizing the obtained sample data (which included the sequenced data) are used to perform validation of a test sample against a reference sample, as claimed.
Similarly, Applicant argues that “Since Walk does not describe sequencing, Walk fails to describe at least the above-emphasized language of amended claim 1” (see Remarks, p. 12). This is unpersuasive, as it appears Applicant has misinterpreted the claim.
To reiterate from above, the data was not subjected to “sequencing” via the “obtaining step”. Instead, the method received already-sequenced data. Therefore, what was being claimed was a simple obtaining of “sequence data”, not that the method step was directed to “sequencing data”. As such, the claim language is what was being described by Walk.
For at least the aforementioned reasons and those set forth in the 103 rejection below, the 103 rejection has been maintained.
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 1-4, 6-20, and 29-30 are rejected under 35 U.S.C. 101 because the claims are directed to a judicial exception (i.e., an abstract idea) without significantly more.
Independent Claims 1 and 29-30 recite validating nucleic acid data by processing the sequence data to obtain determined information indicating a determined source, a determined integrity, or the determined information indicating an determined source and the determined integrity of the sequence data (i.e., a type of analysis), and determining whether the determined information matches the asserted information.
Similarly, dependent Claims 2-3 recite processing the sequence data to determine whether the disease data is indicative of one or more disease features when it is determined that the asserted information matches the determined information.
Dependent Claim 4 recites determining that the asserted information does not match the determined information.
Dependent Claim 6 recites processing the sequence data to obtain determined information indicative of a determined source for the sequence data, and determining whether the determined source matches the asserted source for the sequence data.
Dependent Claim 10 recites processing the sequence data to obtain determined information indicative of a determined integrity of the sequence data, and determining whether the determined integrity matches the asserted integrity for the sequence data.
Dependent Claim 15 recites determining one or more MHC allele sequences from the sequence data and determining whether the one or more MHC alleles sequences match the asserted MHC allele information.
Dependent Claim 16 recites determining MHC allele sequences for six MHC loci from the sequence data.
Dependent Claim 18 recites determining, using the sequence data, a therapy for the subject when it is determined that the asserted information matches the determined information.
Dependent Claim 19 recites determining a plurality of gene group expression levels, and identifying the therapy using the determined gene group expression levels.
These encompass an evaluation, observation, and/or judgment, which falls under the “Mental Processes” grouping of abstract ideas.
With the exception of limitations reciting the use of a computing system and various hardware components, nothing in the claims preclude the claimed steps from being practically performed in the mind. If a claim limitation covers performance of the limitation in the mind but for the recitation of generic computer components, then such claims still fall within the “mental processes” grouping of abstract ideas. Accordingly, the claims recite an abstract idea.
The claims do not recite additional elements that amount to significantly more than the judicial exception. The claims to various computing elements are recited at a high level of generality and recited so generically that they represent no more than mere instructions to apply the judicial exception on a computer (see MPEP 2106.05(f)). These limitations can also be viewed as nothing more than an attempt to generally link the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(h)).
Additionally, the claims recite various insignificant field-of-use limitations, describing only the context rather than a particular manner of achieving the abstract step of determining whether the determined information matches the asserted information. Such field-of-use limitations include
that the nucleic acid data comprises sequence data indicating a nucleotide sequence for at least 5 kilobases (kb) of DNA and/or RNA from a previously obtained biological sample of a subject having, suspected of having, or at risk of having a disease (independent claims 1 and 29-30),
that the information being asserted, determined, and compared relate to a source, integrity, or source and integrity of the sequence data (independent claims 1, 29, and 30 and dependent claims 6 and 10),
that disease features are being identified (dependent claims 2-3),
that the indication includes certain types of data, e.g., the determined information does not match the asserted information, to not process the sequence data in a subsequent analysis, and/or to obtain additional sequence data and/or other information about the biological sample and/or the subject (dependent claim 4),
that the determined information indicative of the determined source for the sequence data is indicative of one, two, or three of a list of information types (dependent claims 7-9),
that the determined information indicative of the determined integrity for the sequence data is indicative of one, two, or three of a list of information types (dependent claims 11-13),
that the asserted information for the sequence data relates to MHC allele information (dependent claims 14-15),
that the MHC allele sequences are for six MHC loci from the sequence data (dependent claim 16),
that the sequence data indicates a nucleotide sequence for RNA and the asserted information indicates whether the RNA is polyA enriched (dependent claim 17),
that the application of the claimed steps relates to determining a therapy for a subject (dependent claim 18), and
that a plurality of gene group expression levels comprising various information are used for identifying the therapy (dependent claim 19).
The claims further recite insignificant extra-solution activities, which represent only nominal or tangential additions to the claims. Such steps include
obtaining nucleic acid data (independent claims 1, 29, and 30), and
generating an indication (upon a determination that the asserted information does not match the determined information) (dependent claims 2-3).
Lastly, dependent claim 20 recites administering a therapy for a subject. This represents nothing more than mere instructions to “apply” the judicial exception in a generic way, and thus does not integrate the mental analysis step into a practical application. See, e.g., MPEP § 2106.05(f) (“Mere Instructions to Apply an Exception”). Additionally, this may be considered as nothing more than an intended use of the claimed invention or a field of use limitation. See, e.g., MPEP § 2106.04(d)(2) (“If the limitation does not actually provide a treatment or prophylaxis, e.g., it is merely an intended use of the claimed invention or a field of use limitation, then it cannot integrate a judicial exception under the ‘treatment or prophylaxis’ consideration”).
Accordingly, the claims are not integrated into a practical application of the idea.
The claims do not recite additional elements that amount to significantly more than the judicial exception.
As discussed above with respect to the integration of the abstract idea into a practical application, the additional elements of various computing hardware components, which amount to no more than mere instructions to apply the exception using generic computer components. Mere instructions to apply an exception using generic computer components cannot provide an inventive concept.
Independent claims 1 and 29-30 recite obtaining (i.e., receiving) data. This is an insignificant extra-solution activities that are well-understood, routine, and conventional. See MPEP 2106.05(d)(II) (“Receiving or transmitting data over a network, e.g., using the Internet to gather data”).
Dependent claims 2-3 recite generating an indication in response to the determination, which is a well-understood, routine, and conventional computing activity. See, e.g., Alice1 at p. 15 (finding that using a computer to obtain data and issue automated instructions are well-understood, routine, and conventional activities)2.
Even when considered as an ordered combination, the claimed elements do not add anything that is not already present when the steps are considered separately. The claims recite a series of abstract steps at a high level of generality, and reciting the generic factors that were involved in some of the identification/determination steps. However, this has previously been found by the courts to be abstract. See, e.g., CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366 (Fed. Cir. 2011) (noting that the claims contained no hint as to how the information regarding Internet transactions were sorted, weighed, and ultimately converted into a useable conclusion that a particular transaction was fraudulent, and thus were even more abstract than the claims in Flook); see also, e.g., Affinity Labs of Texas LLC v. DirecTV., 838 F.3d 1266 (Fed. Cir. 2016) at p. 7-8 (“At that level of generality, the claims do no more than describe a desired function or outcome, without providing any limiting detail that confines the claim to a particular solution to an identified problem. The purely functional nature of the claim confirms that it is directed to an abstract idea, not to a concrete embodiment of that idea”); and Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350 (Fed. Cir. 2016), slip op. 12 (“[The] essentially result-focused, functional character of claim language has been a frequent feature of claims held ineligible under § 101”).
Thus, despite the claims’ attempt to narrow the claims to particular types of information, such limitations do not move the claims outside the realm of abstract ideas. See, e.g., SAP America, Inc. v. InvestPic, LLC, 890 F.3d 1016, 126 USPQ2d 1638 (Fed. Cir. 2018) at p. 12) (finding that the claimed limitations attempting to narrow the claimed statistical methods to bootstrap, jackknife, and cross-validation were all particular methods of resampling, thus doing no more than simply providing further narrowing of what were still mathematical operations, and added nothing outside the abstract realm).
In other words, at this level of generality, the claims do no more than describe a desired function or outcome, and without providing any limiting detail that confines the claims to a particular solution to an identified problem. The purely functional nature of the claims confirm that they are directed to an abstract idea, not to a concrete embodiment of the idea.
A desired goal (i.e., result or effect), absent of structural or procedural means for achieving that goal, is an abstract idea. In this case, the claims are directed to an abstract idea for failing to describe how—by what particular process or structure—the goal is accomplished. Even with the additional elements, the claimed limitations fail to restrict how the goal is accomplished.
Thus, for at least the aforementioned reasons, the claims are rejected under 35 U.S.C. 101 for being directed to a judicial exception (i.e., an abstract idea) without significantly more.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-4, 6-18, and 29-30 are rejected under 35 U.S.C. 103 as being unpatentable over Walk et al. (“Walk”) (US 2008/0234945 A1), in view of Kennedy et al. (“Kennedy”) (US 2018/0321267 A1).
Regarding claim 1: Walk teaches A method, comprising:
obtaining nucleic acid data comprising: sequence data indicating a nucleotide sequence for at least 5 kilobases (kb) of DNA, RNA, or DNA and RNA from a previously obtained biological sample of a subject having, suspected of having, or at risk of having a disease; and asserted information indicating an asserted source, an asserted integrity of the sequence data, or the asserted information indicating an asserted source and the asserted integrity of the sequence data (Walk, [0006] and [0092], where (analyzed) samples, e.g., the reference sample and test sample, comprise at least one compound such as metabolites in a biological sample, the metabolites including RNA or DNA (Walk, [0013]) (i.e., “nucleotide sequence for…DNA and/or RNA”). See Walk, [0001], [0007], [0030], and [0035-0036], where a reference sample is provided and analyzed. Test samples are also provided for analysis.
See Walk, [0196-0197], where the system determines a biomarker specific for a first sample and determines the biomarker based on the trait specific for the first sample. The biomarker may identify an organism or a sample derived there from (e.g., a sample of a particular tissue or cell type, such as a cancer cell or cancerous tissue), indicates a biological source of an organism or a cell, a tissue or an organ thereof, a biomarker for a prevalence for a disease or a disorder, etc.
Note that because both test and reference sample sets of information are utilized for the subsequent validation step, this indicates that the test sample information corresponds to the claimed “sequence data indicating a nucleotide sequence”, and the reference sample analysis corresponding to the claimed “asserted information”, are obtained). See the rejection of the “validation” limitation below for further detail).
Although Walk does not appear to explicitly state the size of the RNA/DNA sequences (i.e., being “at least 5 kilobases (kb)” as claimed), one of ordinary skill in the art would have recognized that the various steps of obtaining, analyzing, and validating the data would have been performed the same regardless of the specific size of the nucleic acid sequence involved. Therefore, one of ordinary skill in the art would have found it obvious to have modified Walk such that the sequence is at least 5 kb, as claimed, with the motivation of potentially greater accuracy in drawing conclusions/assessments (e.g., longer genetic sequences may be better indicators of certain conclusions/results than shorter sequences)); and
validating the nucleic acid data by:
processing the sequence data to obtain determined information indicating a determined source … of the sequence data; and determining whether the determined information matches the asserted information (Walk, [0001], where the test sample and reference sample are analyzed in an identical sequence; thus, see Walk, [0196-0197] above with regards to the “processing the sequence data to obtain determined information indicating a determined source” step. See Walk, [0007], [0030], and [0035-0036], where a test sample and reference sample are analyzed and compared in order to validate the raw results, i.e., where the results of the actual analysis (i.e., “determined information”) and the results of a previous analysis for the same reference sample obtained from the reference sample (i.e., “asserted information”) are compared by assessing whether the samples are different or identical to each other (i.e., “determining whether the determined information matches the asserted information”). See also Walk, [0133], where raw results of a sample may be invalidated if the monitored process parameters are inconsistent).
Walk does not appear to explicitly teach using at least one computer hardware processor to perform [the claimed steps]; [and the asserted/determined information indicating] a determined integrity, a determined integrity of the sequence data, or the determined information indicating a determined source and the determined integrity [of the data].
Kennedy teaches using at least one computer hardware processor to perform [the claimed steps] (Kennedy, [0104] and [0110], where the disclosed system may be implemented by one or more storage devices and memory that holds software executable on a processor for implementing the disclosed steps); [and]
the asserted/determined information indicating] a determined integrity, a determined integrity of the sequence data, or the determined information indicating a determined source and the determined integrity [of the data] (Kennedy, [0069-0070], where the system analyzes the biological sample in order to determine the level(s) of the one or more biomarkers in the sample. After the level(s) of the one or more sample quality biomarkers in a sample are determined, the measured level(s) are compared to reference levels characteristic of a sample in compliance with a protocol (i.e., “positive” or “acceptable” sample quality), and/or reference levels characteristic of a sample not in compliance with a protocol (i.e., “negative” or “not acceptable” sample quality). Levels of the one or more biomarkers matching the reference levels characteristic of a sample positive for sample quality or a sample quality parameter are indicative of acceptable sample quality or quality parameter).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Walk and Kennedy (hereinafter “Walk as modified”) with the motivation of assessing whether samples meet the quality standard in order to avoid waste of resources and ensure that valid results are generated.
Furthermore, it would have been obvious to one of ordinary skill in the art to have incorporated Kennedy’s processor, as a processor would have had to exist within Walk’s disclosure, otherwise Walk’s claimed computer would have inoperable to carry out any of the disclosed computing functions/steps. Therefore, although Walk does not appear to explicitly disclose a processor as claimed, one of ordinary skill in the art would have found it obvious to have incorporated Kennedy’s processor into Walk’s system with the motivation of enabling Mosher’s systems to execute the disclosed steps.
Regarding claim 2: Walk as modified teaches The method of claim 1, further comprising:
processing the sequence data to determine whether the sequence data is indicative of one or more disease features when it is determined that the asserted information matches the determined information (Walk, [0036], where the disclosed system draws conclusions based on the validated results (i.e., “when it is determined that the asserted information matches the determined information”) with respect to the presence or absence of at least one specific compound or its chemical nature. See also Walk, [0074], where analyzing includes generating a specific profile (i.e., a fingerprint) for a certain sample based on the validated raw results. See Walk, [0268], where examples of profiles are biological marker (i.e., biomarker) profiles. See Walk, [0203], where the biomarker may be suitable for diagnostic purposes, where due to the determination of a biomarker, a disease, disorder, or prevalence therefore can be diagnosed, which comprises the aforementioned steps (e.g., see cited portions of Walk in claim 1 above for further detail); note that Walk further alludes to this application to diagnostics in [0004], by stating that “it would be highly desirable to reliably apply metabolome analysis techniques for various emerging tasks including…diagnostics”).
Regarding claim 3: Walk as modified teaches The method of claim 1, further comprising:
determining that the determined information matches the asserted information; and processing the sequence data to determine whether it is indicative of one or more disease features (Walk, [0036], where the disclosed system draws conclusions based on the validated results (i.e., “when it is determined that the asserted information matches the determined information”) with respect to the presence or absence of at least one specific compound or its chemical nature. See also Walk, [0074], where analyzing includes generating a specific profile (i.e., a fingerprint) for a certain sample based on the validated raw results. See Walk, [0268], where examples of profiles are biological marker (i.e., biomarker) profiles. See Walk, [0203], where the biomarker may be suitable for diagnostic purposes, where due to the determination of a biomarker, a disease, disorder, or prevalence therefore can be diagnosed, which comprises the aforementioned steps (e.g., see cited portions of Walk in claim 1 above for further detail); note that Walk further alludes to this application to diagnostics in [0004], by stating that “it would be highly desirable to reliably apply metabolome analysis techniques for various emerging tasks including…diagnostics”).
Regarding claim 4: Walk as modified teaches The method of claim 1, further comprising:
generating an indication of at least one of: that the determined information does not match the asserted information, to not process the sequence data in a subsequent analysis, or to obtain additional sequence data or other information about the biological sample or the subject, when it is determined that the asserted information does not match the determined information (Kennedy, [0098], where sample quality information for the sample(s) may be compiled into a single document or report, which may include a total number of different sample quality biomarkers detected, a listing of sample quality biomarkers associated with one or more sample quality parameters, identification of which sample quality biomarkers in the identified sample quality parameters were present in aberrant levels, an indication of whether each aberrant sample quality biomarker is present at a level higher or lower than the standard range, an indication of whether the value for each sample quality parameter composite score is within the range of the reference score, a list of affected sample quality parameters, etc.).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Walk and Kennedy with the motivation of informing users of the results of the analysis, as well as informing the computer what next steps should be taken.
Regarding claim 6: Walk as modified teaches The method of claim 1, wherein the asserted information indicates the asserted source of the sequence data, the method further comprising:
processing the sequence data to obtain determined information indicative of a determined source for the sequence data; and determining whether the determined source matches the asserted source for the sequence data (Walk, [0197], where the system may determine a biomarker specific for a first sample, and specifically identifies an organism or a sample derived there from (e.g., a sample of a particular tissue or cell type, such as a cancer cell or cancerous tissue), indicates a biological source of an organism or a cell, a tissue or an organ thereof, a biomarker for a prevalence of a disease or a disorder, etc. See Walk, [0035-0036], where analyzing includes validating results obtained from the reference samples, i.e., that the results of the actual analysis and the results of a previous analysis for the same reference sample are different or identical to each other. This implies that biomarkers, which are part of the data included within the sample (and by extension, reference sample) may also be compared (i.e., “determining whether the determined source matches the asserted source for the sequence data”)).
Regarding claim 7: Walk as modified teaches The method of claim 6, wherein the determined information indicative of the determined source for the sequence data is indicative of at least one of an MHC genotype of the subject; whether the nucleic acid data is RNA data or DNA data; a tissue type of the biological sample; a tumor type of the biological sample; a sequencing platform used to generate the sequence data; SNP concordance; or whether an RNA sample is polyA enriched (Walk, [0197], where the system determines a biomarker specific for a first sample, where the biomarker may identify an organism or a sample derived there from (e.g., a sample of a particular tissue or cell type, such as a cancer cell or cancerous tissue) (i.e., “tumor type of the biological sample”), indicates a biological source of an organism or a cell, a tissue or an organ thereof (i.e., “tissue type of the biological sample”), a biomarker for a prevalence for a disease or a disorder, etc.).
Regarding claim 8: Walk as modified teaches The method of claim 7, wherein the determined information indicative of the determined source for the sequence data is indicative of at least two of an MHC genotype of the subject; whether the nucleic acid data is RNA data or DNA data; a tissue type of the biological sample; a tumor type of the biological sample; a sequencing platform used to generate the sequence data; SNP concordance, or whether an RNA sample is polyA enriched (Walk, [0197], where the system determines a biomarker specific for a first sample, where the biomarker may identify an organism or a sample derived there from (e.g., a sample of a particular tissue or cell type, such as a cancer cell or cancerous tissue) (i.e., “tumor type of the biological sample”), indicates a biological source of an organism or a cell, a tissue or an organ thereof (i.e., “tissue type of the biological sample”), a biomarker for a prevalence for a disease or a disorder, etc.).
Regarding claim 9: Walk as modified teaches The method of claim 8, wherein the determined information indicative of the determined source for the sequence data is indicative of at least three of an MHC genotype of the subject; whether the nucleic acid data is RNA data or DNA data; a tissue type of the biological sample; a tumor type of the biological sample; a sequencing platform used to generate the sequence data; SNP concordance, or whether an RNA sample is polyA enriched (Walk, [0197], where the system determines a biomarker specific for a first sample, where the biomarker may identify an organism or a sample derived there from (e.g., a sample of a particular tissue or cell type, such as a cancer cell or cancerous tissue) (i.e., “tumor type of the biological sample”), indicates a biological source of an organism or a cell, a tissue or an organ thereof (i.e., “tissue type of the biological sample”), a biomarker for a prevalence for a disease or a disorder, etc. See Walk, [0079], where the system determines the presence or absence or the amount of a portion of metabolites, including RNA or DNA (see Walk, [0013]), and may analyze the metabolome by comparing the metabolites, amounts of metabolites, or the metabolic profile of different samples (i.e., given that the system indicates the presence/absence of metabolites, this would mean that it would indicate the metabolites are RNA data or DNA data, as claimed)).
Regarding claim 10: Walk as modified teaches The method of claim 1, wherein the asserted information indicates the asserted integrity of the sequence data, the method further comprising:
processing the sequence data to obtain determined information indicative of a determined integrity of the sequence data; and determining whether the determined integrity matches the asserted integrity for the sequence data (Kennedy, [0069-0070], where the system analyzes the biological sample in order to determine the level(s) of the one or more biomarkers in the sample. After the level(s) of the one or more sample quality biomarkers in a sample are determined, the measured level(s) are compared to reference levels characteristic of a sample in compliance with a protocol (i.e., “positive” or “acceptable” sample quality), and/or reference levels characteristic of a sample not in compliance with a protocol (i.e., “negative” or “not acceptable” sample quality). Levels of the one or more biomarkers matching the reference levels characteristic of a sample positive for sample quality or a sample quality parameter are indicative of acceptable sample quality or quality parameter).
Regarding claim 11: Walk as modified teaches The method of claim 10, wherein the determined information indicative of the determined integrity is indicative of total sequence coverage; exon coverage; chromosomal coverage; a ratio of nucleic acids encoding two or more subunits of a multimeric protein; species contamination; single nucleotide polymorphisms (SNPs); complexity; or guanine (G) and cytosine (C) percentage (%) of the sequence data (Kennedy, [0010], where the quality criteria/parameters may include sample processing time, sample storage temperature, etc.).
Although Walk as modified does not appear to explicitly state that the quality information includes that being claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Regarding claim 12: Walk as modified teaches The method of claim 11, wherein the determined information indicative of the determined integrity is indicative of at least two of total sequence coverage; exon coverage; chromosomal coverage; a ratio of nucleic acids encoding two or more subunits of a multimeric protein; species contamination; single nucleotide polymorphisms (SNPs); complexity; or guanine (G) and cytosine (C) percentage (%) of the sequence data (Kennedy, [0010], where the quality criteria/parameters may include sample processing time, sample storage temperature, etc.).
Although Walk as modified does not appear to explicitly state that the quality information includes that being claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Furthermore, one of ordinary skill in the art would have found it obvious to have included more than one of these factors with the motivation of potentially increased accuracy, e.g., the more dimensions being compared, the likelihood that the accuracy is higher.
Regarding claim 13: Walk as modified teaches The method of claim 12, wherein the determined information indicative of the determined integrity is indicative of at least three of total sequence coverage; exon coverage; chromosomal coverage; a ratio of nucleic acids encoding two or more subunits of a multimeric protein; species contamination; single nucleotide polymorphisms (SNPs); complexity; or guanine (G) and cytosine (C) percentage (%) of the sequence data ((Kennedy, [0010], where the quality criteria/parameters may include sample processing time, sample storage temperature, etc.).
Although Walk as modified does not appear to explicitly state that the quality information includes that being claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Furthermore, one of ordinary skill in the art would have found it obvious to have included more than one of these factors with the motivation of potentially increased accuracy, e.g., the more dimensions being compared, the likelihood that the accuracy is higher.
Regarding claim 14: Walk as modified teaches The method of claim 1, wherein the asserted information for the sequence data comprises MHC allele information for the subject (Walk, [0013], where metabolites include peptides, oligopeptides, polypeptides, oligonucleotides, and polynucleotides such as RNA or DNA).
Although Walk as modified does not appear to explicitly state that the asserted information for the sequence data includes MHC allele information for the subject as claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Regarding claim 15: Walk as modified teaches The method of claim 1, further comprising:
determining one or more MHC allele sequences from the sequence data (Walk, [0021], where the system determines at least one compound including determining at least one characteristic feature of the at least one compound comprised by the sample. See Walk, [0012-0013], where compounds may be metabolites, and metabolites may include peptides, oligopeptides, polypeptides, oligonucleotides, and polynucleotides, such as RNA or DNA) and determining whether the one or more MHC alleles sequences match the asserted MHC allele information for the subject (Walk, [0007], [0030], and [0035-0036], where a test sample and reference sample are analyzed and compared in order to validate the raw results, i.e., where the results of the actual analysis and the results of a previous analysis for the same reference sample obtained from the reference sample are compared by assessing whether the samples are different or identical to each other. See also Walk, [0133], where raw results of a sample may be invalidated if the monitored process parameters are inconsistent).
Although Walk as modified does not appear to explicitly state that the asserted information for the sequence data includes MHC allele information for the subject as claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Regarding claim 16: Walk as modified teaches The method of claim 15, wherein determining the one or more MHC allele sequences comprises determining MHC allele sequences for six MHC loci from the sequence data (Walk, [0021], where the system determines at least one compound including determining at least one characteristic feature of the at least one compound comprised by the sample. See Walk, [0012-0013], where compounds may be metabolites, and metabolites may include peptides, oligopeptides, polypeptides, oligonucleotides, and polynucleotides, such as RNA or DNA).
Although Walk as modified does not appear to explicitly state that the asserted information for the sequence data includes MHC allele sequences for six MHC loci as claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Regarding claim 17: Walk as modified teaches The method of claim 1, wherein the sequence data indicates the nucleotide sequence for RNA, the asserted information indicates whether the RNA is polyA enriched (Walk, [0079], where the system determines the presence or absence or the amount of a portion of metabolites, including RNA or DNA (see Walk, [0013]), and may analyze the metabolome by comparing the metabolites, amounts of metabolites, or the metabolic profile of different samples (i.e., given that the system indicates the presence/absence of metabolites, this would mean that it would indicate the metabolites are RNA data or DNA data, as claimed)).
Although Walk as modified does not appear to explicitly state that “the asserted information indicates whether the RNA is polyA enriched” as claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Walk as modified’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
Regarding claim 18: Walk as modified teaches The method of claim 1, further comprising:
determining, using the sequence data, a therapy for the subject when it is determined that the asserted information matches the determined information (Walk, [0202], where a biomarker may be determined, which may serve as standards based on which suitable therapies or suitable dosages for a drug in a therapy may be determined, and preferably is used to predict an organism’s response to a drug, and therefore may be used to select a suitable therapy. See Walk, [0036], [0074], [0203], and [0268] in claim 2 above with regards to “when it is determined that the asserted information matches the determined information”).
Regarding claim 29: Claim 30 recites substantially the same claim limitations as claim 1, and is rejected for the same reasons.
Note that Kennedy teaches A system comprising: at least one computer hardware processor; at least one non-transitory computer-readable storage medium storing processor executable instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform a method, comprising [the claimed steps] (Kennedy, [0104], where the disclosed system may be implemented as a computing device that includes one or more non-transitory computer-readable media for storing one or more computer-executable instructions or software for implementing the disclosed steps, where the computing device 100 includes a processor 102 for executing the computer-readable and computer-executable instructions or software stored in the memory 106).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Walk and Kennedy to include a computer-readable storage medium embodiment with the motivation of persisting such logic such that it can be reused, re-executed, etc.
Regarding claim 30: Claim 30 recites substantially the same claim limitations as claim 1, and is rejected for the same reasons.
Note that Kennedy teaches At least one non-transitory computer-readable storage medium storing processor executable instructions that, when executed by at least one computer hardware processor, cause the at least one computer hardware processor to perform a method, comprising [the claimed steps] (Kennedy, [0104], where the disclosed system may be implemented as a computing device that includes one or more non-transitory computer-readable media for storing one or more computer-executable instructions or software for implementing the disclosed steps, where the computing device 100 includes a processor 102 for executing the computer-readable and computer-executable instructions or software stored in the memory 106).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Walk and Kennedy to include a computer-readable storage medium embodiment with the motivation of persisting such logic such that it can be reused, re-executed, etc.
Claims 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Walk et al. (“Walk”) (US 2008/0234945 A1), in view of Kennedy et al. (“Kennedy”) (US 2018/0321267 A1), in further view of Kennedy et al. (“Chudova”) (US 2019/0100809 A1).
Regarding claim 19: Walk as modified teaches The method of claim 18, but does not appear to explicitly teach wherein determining the therapy comprises: determining a plurality of gene group expression levels, the plurality of gene group expression levels comprising a gene group expression level for each gene group in a set of gene groups, wherein the set of gene groups comprises at least one gene group associated with cancer malignancy, and at least one gene group associated with cancer microenvironment; and identifying the therapy using the determined gene group expression levels.
Chudova teaches wherein determining the therapy comprises: determining a plurality of gene group expression levels, the plurality of gene group expression levels comprising a gene group expression level for each gene group in a set of gene groups, wherein the set of gene groups comprises at least one gene group associated with cancer malignancy, and at least one gene group associated with cancer microenvironment; and identifying the therapy using the determined gene group expression levels (Chudova, [0009], where the disclosed system determines an expression level for one or more gene expression products from a tissue sample, e.g., thyroid tissue sample; compare the expression level with gene expression data obtained from a plurality of reference samples; and based on correlating, identifying the tissue sample as malignant (i.e., “at least one gene group associated with cancer malignancy”). Note that gene expression products comprise two or more genes (see, e.g., Chudova, [0008]), and thus correspond to the claimed “gene group”. See Chudova, [0010], where a treatment is selected based on comparing the gene expression data for each set of biomarkers comprising one or more refence gene expression levels correlated with the presence of one or more tissue types (i.e., “associated with cancer malignancy”) including follicular thyroid adenoma, follicular thyroid carcinoma, nodular hyperplasia, etc.).
Although Chudova does not appear to explicitly state that the information pertains to a “cancer microenvironment” as claimed, the claimed invention does not distinguish over the prior art because the differences in the claim limitations and the prior art’s disclosure are only found in the nonfunctional descriptive material are not functionally involved in the steps recited. The parent claims’ steps of obtaining, comparing, and determining matching information would have been performed the same regardless of the specific type of information involved. Thus, this descriptive material will not distinguish the claimed invention from the prior art in terms of patentability. See In re Gulack, 703 F.2d 1381, 1385, 217 USPQ2d 401, 404 (Fed. Cir. 1983); In re Lowry, 32 F.3d 1579, 32 USPQ2d 1031 (Fed. Cir. 1994).
Therefore, it would have been obvious to a person of ordinary skill in the art to have referred to Chudova’s teachings in making the claimed invention, because such data does not functionally relate to the steps in the method claimed and because the subjective interpretation of the data does not patentably distinguish the claimed invention over the prior art.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Walk as modified and Chudova (hereinafter “Walk as modified”) with the motivation of providing improved diagnostic power, lower likelihood of false positives or false negative, and/or greater statistical confidence levels (Chudova, [0182]).
Regarding claim 20: Walk as modified teaches The method of claim 19, further comprising administering the therapy to the subject (Chudova, [0010] and [0265-0266], where a selected treatment includes administering a therapeutic agent).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Walk as modified and Chudova with the motivation of leveraging from the improved diagnostic power of gene expression products (see Chudova, [0182]), to effect improved patient outcomes/treatments for better patient care.
Conclusion
THIS ACTION IS MADE FINAL. 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.
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/IRENE BAKER/Primary Examiner, Art Unit 2154
15 April 2026
1 Alice Corp. v. CLS Bank Int'l, 573 U.S. __, 134 S. Ct. 2347 (2014)
2 See Alice at p. 15: “Using a computer to create and maintain ‘shadow’ accounts amounts to electronic recordkeeping—one of the most basic functions of a computer…. The same is true with respect to the use of a computer to obtain data, adjust account balances, and issue automated instructions; all of these computer functions are ‘well-understood, routine, conventional activit[ies]’ previously known to the industry…. In short, each step does not do more than require a generic computer to perform generic computer functions”.
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