DETAILED ACTION
Applicant’s response filed 04/01/2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 3-5, 9, 13-14 and 16-20 are cancelled by Applicant.
Claims 1-2, 6-8, 10-12, 15 and 21-22 are currently pending.
Claims 6 and 8 are withdrawn by Applicant as discussed in the Election of Species section in the Office Action mailed 12/11/2024.
Claims 1-2, 7, 10-12, 15 and 21-22 are herein under examination.
Claims 1-2, 7, 10-12, 15 and 21-22 are rejected.
Claims 1, 12 and 21 are objected.
Priority
The instant application claims domestic benefit to U.S. Provisional Application No. 63/022,296 filed 05/08/2020. The claim to domestic benefit is acknowledged. As such, the effective filing date for claims 1-2, 7, 10-12, 15 and 21-22 is 05/08/2020.
Information Disclosure Statement
The IDS filed 01/15/2026, 01/22/2026, 04/01/2026 and 05/28/2026 follow the provisions of 37 CFR 1.97 and have been considered in full. A signed copy of the list of references cited from these IDS is included with this Office Action.
Withdrawn Rejections
35 USC 112(b)
The rejection of claims 1-2, 7, 10-13, 15 and 21-22 under 35 USC 112(b) is withdrawn in view of claim amendments.
35 USC 112(d)
The rejection of claim 13 under 35 USC 112(d) is withdrawn because Applicant canceled the claim.
35 USC 101
The rejection of claim 13 under 35 USC 101 is withdrawn because Applicant canceled the claim.
35 USC 103
The rejection of claims 1-2, 7, 12-13 and 22 under 35 USC 103 as being unpatentable over Wu et al. in view of Panyukov et al., Saingam et al., Kraken Manual, and Breitwieser et al. in view of claim amendments and Applicant’s persuasive argument regarding none of the cited references disclosing separate hash tables for pathogen and control k-mers nor a dual-threshold architecture used to provide a positive detection output (pg. 15, last para. – pg. 16, para. 1 of Remarks filed 04/01/2026).
The rejection of claims 10 and 15 under 35 USC 103 as being unpatentable over Wu et al. in view of Panyukov et al., Saingam et al., Kraken Manual, and Breitwieser et al. and in further view of Wohl et al. for the same reasons applied above to claims 1 and 12.
The rejection of claim 11 under 35 USC 103 as being unpatentable over Wu et al. in view of Panyukov et al., Saingam et al., Kraken Manual, and Breitwieser et al. and in further view of Kang et al. for the same reasons applied above to claim 1.
The rejection of claim 21 under 35 USC 103 as being unpatentable over Wu et al. in view of Panyukov et al., Saingam et al., Kraken Manual, Breitwieser et al., and Gardner in view of claim amendments and Applicant’s persuasive argument regarding none of the cited references disclosing separate hash tables for pathogen and control k-mers nor a dual-threshold architecture used to provide a positive detection output (pg. 15, last para. – pg. 16, para. 1 of Remarks filed 04/01/2026).
Claim Objections
The objection to claims 1, 12 and 21 are withdrawn in view of claim amendments.
Claims 1, 12 and 21 are objected to because of the following informalities:
Claim 1, pg. 3, line 17, should recite a comma after “that”.
Claim 12, pg. 5, line 10, should recite a comma before “wherein”.
Claim 12, pg. 5, lines 22-23, should recite “and count of the second k-mers being above a second threshold count” to correct grammar and clarify the phrase.
Claim 12, pg 5, last line, should recite “of the subset”.
Claim 21, pg. 6, line 11, should recite “; and”.
Claim 21, pg. 7, line 1, recites “identifying” which should be deleted.
Claim 21, pg. 7, lines 4-8, should be indented to the same degree as the other sub-steps of “using a processor”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
35 USC 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-2, 7, 10-11 and 21-22 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
This rejection is newly recited as necessitated of claim amendment.
Claims dependent from a rejected claim are also rejected unless otherwise noted.
Claim 1, pg. 4, line 2, recites “the positive detection output for each individual biological sample of a subset” which lacks antecedent basis. Claim 1, pg. 3, lines 22-24, recites a positive detection output for an individual biological sample of the plurality of biological samples, but there is no recitation of a positive detection output for each individual biological sample of a subset. Provide antecedent basis for the recitation.
Claim 1 (pg. 4, line 3) and claim 11 recites “the positive detection output” which renders the claims indefinite. It is unclear if the recitation refers to claim 1, pg. 3, lines 22-24, of “a positive detection output ... for the individual biological sample of the plurality of biological samples” or claim 1, pg. 4, line 2, of “the positive detection output for each individual biological sample of a subset”. Clarify which output is being referenced.
Claim 21, pg. 7, line 13 recites “the positive detection output for each individual biological sample of a subset” which lacks antecedent basis. Claim 21, pg. 7, lines 9-11 recites “a positive detection output … for the individual biological sample of the plurality of biological samples”, but there is no recitation of a positive detection output for each individual biological sample of a subset. Provide antecedent basis for the recitation.
Claim 22 recites “the positive detection output is provided for the individual biological sample of the subset” which renders the claim indefinite. It is unclear which positive detection output for which individual biological sample of the subset is being referenced because claim 1, pg. 4, line 2, recites a positive detection output for each individual biological sample of a subset. Clarify which output and which individual biological sample of the subset is being referenced.
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 1-2, 7, 10-12, 15 and 21-22 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 1:
Step 1 asks whether the claims recite statutory subject matter. In the instant application, claims 1-2, 7, 10-11 and 22 recite a method, claims 12 and 15 recite a method, and claim 21 recite a method. As such, these claims recite statutory subject matter (Step 1: YES).
Step 2A, Prong 1:
Claims that recite statutory subject matter are analyzed under Step 2A, Prong 1 to determine if they recite any concepts that equate to an abstract idea, law of nature or natural phenomena. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 1 recites “counting, in real-time, first k-mers in the sequence data that have an exact match in the first hash table to generate a first count of exact matches of the first k-mers; counting, in real-time, second k-mers in the sequence data that have an exact match in the second hash table to generate a second count of exact matches of the second k-mers; determining that, for an individual biological sample of the plurality of biological samples, the first count of exact matches of the first k-mers in the sequence data is above a first threshold and the second count of exact matches of the second k-mers in the sequence data is
Claim 2 recites “wherein the first k-mers or the second k-mers in the sequence data are of a fixed size that is greater than 24 nucleotides.”
Claim 10 recites “comprising identifying sequence variants of the pathogen in aligned sequence data.”
Claim 12 recites “counting first k-mers in the sequence data, in real-time, that have an exact match in the first hash table to generate a first count of exact matches of the first k-mers;
Claim 15 recites “identifying sequence variants of the pathogen in the sequence data.”
Claim 21 recites “counting, in real-time, first k-mers in the sequence data that have an exact match in the first hash table to generate a first count of exact matches of the first k-mers; counting, in real-time, identifying second k-mers in the sequence data that have an exact match in the second hash table to generate a second count of exact matches of the second k-mers; determining that, for an individual biological sample of the plurality of biological samples, the first count of exact matches of the first k-mers in the sequence data is above a first threshold and the second count of exact matches of the second k-mers in the sequence data is above a second threshold; providing a positive detection output based on the first count and the second count being above the respective first and second threshold for the individual biological sample of the plurality of biological samples; initiating sequence alignment with the genome of the pathogen upon providing the positive detection output for each individual biological sample of a subset of the plurality of biological samples; and not performing sequencing alignment with the genome of the pathogen for biological samples of the plurality of biological samples not in the subset.”
Claim 22 recites “wherein the positive detection output is provided for the individual biological sample of the subset while sequence data is still being generated by the sequence device and based on detection of 1-5% of a total number of the amplicons of the individual biological sample of the subset.”
Limitations reciting a mental process.
The above cited limitations in claims 1, 10, 12, 15 and 21-22 are recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind or by a human using pen and paper. The paragraphs below discuss the limitations in these claims that recite a mental process under their broadest reasonable interpretation (BRI).
Regarding claims 1, 12 and 21, determining that a first and a second count od k-mers are above respective count threshold includes comparing data. Providing a positive detection output includes displaying the results of the of abstract idea of determining the counts are above a threshold. Terminating counting k-mers upon a positive detection includes stopping counting k-mers from the sequence data. Initiating sequence alignment includes comparing sequences which can be done on pen and paper (claims 1 and 21). Terminating sequence analysis of the sequence data includes not performing any further actions on the previously generated sequence data (claim 12). Not performing sequencing alignment includes making a mental determination to not perform sequence alignment (claim 21).
Regarding claims 10 and 15, identifying sequence variants in the aligned sequenced data includes analyzing previously aligned sequence data.
Limitations reciting a mathematical concept.
The above cited limitations in claims 1, 12 and 21 equate to a mathematical concept because they are similar to the concept of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. Regarding claims 1, 12 and 21, counting k-mers using a hash table to generate a k-mer count includes a mathematical concept of counting k-mers to generate a number. It also includes using a hash function.
Limitations included in the judicial exception.
Claims 2 and 22 are included in the recited judicial exception in claim 1 of counting k-mers and providing a detection output, respectively, because they further limit judicial exception.
As such, claims 1-2, 7, 10-12, 15 and 21-22 recite an abstract idea (Step 2A, Prong 1: YES).
Additional Elements:
Once limitations have been identified that recite a judicial exception, the claims are evaluated for additional elements. The additional elements are then analyzed under Step 2A, Prong 2 then Step 2B. The instant claims recite the following additional elements:
Claim 1 recites “generating a first hash table that is initialized with a set of reference k-mers comprising a subset of all k-mers in a genome of a pathogen, wherein the subset is selected based on k-mers with no exact match in a human control genome; generating a second hash table initialized with control k-mers of the human control genome; receiving streaming sequence data from a flow cell of a sequence device operating to conduct a sequencing run on a plurality of biological samples simultaneously in parallel, wherein the sequence data comprises amplicon sequences from amplicons generated from the plurality of biological samples;”
Claim 7 recites “wherein the set of reference k-mers is larger than the set of control k-mers.”
Claim 11 recites “comprising administering a treatment for the pathogen responsive to the positive detection output for the pathogen detection, wherein the pathogen is SARS-CoV-2, and wherein the treatment is a SARS-CoV-2 treatment.
Claim 12 recites “generating a first hash table that is initialized with a set of reference k-mers comprising a subset of all k-mers in a genome of a pathogen, wherein the subset is selected based on k-mers with no exact match in a human control genome; generating a second hash table initialized with control k-mers of the human control genome; generating sequence data from a flow cell of a sequence device operating to conduct a sequencing run on a sequencing library prepared from a plurality of biological samples simultaneously in parallel wherein the sequence data comprises amplicon sequences from amplicons generated from the plurality of biological samples;”
Claim 21 recites “generating a first hash table that is initialized with a set of reference k-mers comprising a subset of all k-mers in a genome of a pathogen, wherein the subset is selected based on k-mers with no exact match in a human control genome; generating a second hash table initialized with control k-mers of the human control genome; receiving streaming sequence data from a flow cell of a sequence device operating to conduct a sequencing run on a plurality of biological samples simultaneously in parallel, wherein the sequence data comprises amplicon sequences from amplicons generated from the plurality of biological samples; using a processor comprising a reconfigurable field-programmable gate array to execute steps comprising:”
These above recited additional elements are analyzed below under both Step 2A, Prong 2 and Step 2B:
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” (MPEP § 2106.05(f)) and to insignificant extra-solution activity (MPEP § 2106.05(g)). The paragraphs below discuss the additional elements recited above in the instant claims.
Claims 1, 7, 12 and 21 recite generating hash tables containing pathogen and control k-mers, receiving streaming sequence data, and generating sequence data. These limitations equate to data gathering which the courts have established as insignificant-extra solution activity in Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015). These limitations collect data used in the judicial exceptions in claims 1, 12 and 21 of counting k-mers, terminating counting k-mers, terminating analysis of the sequence data, and initiating sequence alignment. These limitations then output the result of the judicial exception.
Claim 11 recites administering a SARS-CoV-2 treatment, this limitation equates to the words “apply it” because it generally recites an effect of the judicial exception and claims every mode of accomplishing that effect (MPEP 2106.05(f)(3)). The “treatment” is also so generically recited that it encompasses all types of treatments and thus is not a particular treatment (MPEP 2106.04(d)(2)(a)).
Claim 21 uses a processor comprising an FPGA to perform the judicial exception of counting k-mers, providing a detection output, and initiating sequence alignment. This limitation equates to the words “apply it”, which does not integrate a judicial exception into a practical application. MPEP 2106.05(f) recites “[a]s explained by the Supreme Court, in order to make a claim directed to a judicial exception patent-eligible, the additional element or combination of elements must do ‘more than simply stat[e] the [judicial exception] while adding the words ‘apply it’". Alice Corp. v. CLS Bank, 573 U.S. 208, 221, 110 USPQ2d 1976, 1982-83 (2014) (quoting Mayo Collaborative Servs. V. Prometheus Labs., Inc., 566 U.S. 66, 72, 101 USPQ2d 1961, 1965).
As such, claims 1-2, 7, 10-12, 15 and 21-22 are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions “to apply” the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The paragraphs below discuss the additional elements recited above in the instant claims.
Claims 1 and 21 recite receiving streaming sequence data. The BRI of this limitation includes it being computer-implemented, especially because the specification states that the instant claims can be performed on a computer [7] [38] [47]. Therefore, these limitations equate to receiving/transmitting data over a network, which the courts have established as WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014).
Claims 11 and 21 recite a processor comprising an FPGA and administering a SARS-CoV-2 treatment, respectively. These limitations equate to the words “apply it”, as discussed above in section Step 2A, Prong 2. MPEP 2106.05(f)(1) recites that limitations that equate to the words “apply it” do not provide significantly more under Step 2B.
Claim 12 recites generating sequence data which equates to a WURC limitation because the specification discloses various commercially available sequencing techniques such as Ion Torrent [37].
Claims 1, 7, 12 and 21 recite generating hash tables containing pathogen and control k-mers. The BRI of these limitations include storing data in memory, which the courts have established as a WURC function of a generic computer in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
When claim 1, 12 and 21 limitations of generating hash tables comprising genomic data in combination with a FPGA and a generic computer are viewed in combination, they equate to WURC limitations as taught by Aluru et al. (“Aluru”; A review of hardware acceleration for computational genomics. IEEE Design & Test 31, no. 1 (2013): 19-30; previously cited on PTO92 mailed 10/01/2025) and Donato et al. (“Donato”; BWaveR: an FPGA-accelerated genomic sequence mapper leveraging succinct data structures. (2018); previously cited on PTO892 mailed 10/01/2025). Aluru surveys the use of FPGAs in the area of biological sequence analysis, particularly in computational genomics, as well as in the field of high-throughput sequencing (abstract). Aluru shows generating hash tables with genomic data (pg. 7, col. 1, para. 1) to perform mapping between a genome of an individual and a template genome, wherein the mapping is performed using the FPGA (pg. 6, col. 2, last para.).
Donato teaches “k-mers are used as keys for indexing a hash table, whose elements store the positions of the occurrences of the correspondent k-mers in the reference sequence, together with the symbols that precede and succeed the k-mers in those positions” (pg. 69, last para.). Donato also teachings using a CPU and FPGA together, where the CPU performs Burrows-Wheeler Transformation of the reference genome and the FPGA performs read mapping (pg. 4, para. 2).
When Aluru and Donato are taken together, they demonstrate that storing genomic data in a hash table is WURC when viewed in combination with a generic computer and a FPGA.
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they equate to WURC functions and/or components of a generic computer and/or generic computing system and to mere instructions “to apply” an exception, which cannot provide significantly more. These additional elements also equate to WURC limitations of hash tables in combination with genomic data, FPGAs, and CPUs as taught above by Aluru and Donato. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: NO).
As such, claims 1-2, 7, 10-12, 15 and 21-22 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 04/01/2026 have been fully considered but they are not persuasive.
Applicant argues counting first and second k-mers in real-time using separate hash tables from sequencing data containing a plurality of biological samples is not a mental process (pg. 9, last para. – pg. 10, para. 1). Applicant’s argument is persuasive because a human cannot practically count different sets of k-mers using separate hash tables in real-time from different biological samples. However, counting k-mers using the first/second hash table still recites a mathematical concept.
Applicant argues that claims 1, 12 and 21 merely involve mathematical concepts but do not recite them (pg. 10, para. 3). Applicant’s argument is not persuasive because:
Claims 1, 12 and 21 recite counting k-mers using hash tables to generate k-mer counts. This recites a mathematical concept. K-mer counting using a hash table requires a hash function and requires counting to generate a number (i.e., k-mer count). MPEP 2106.04(a)(2)(I)(C) recites “A mathematical calculation is a mathematical operation (such as multiplication) or an act of calculating using mathematical methods to determine a variable or number … a claim does not have to recite the word ‘calculating’ in order to be considered a mathematical calculation. For example, a step of ‘determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations.”
Applicant argues improvement for more rapid, accurate and sensitive pathogen detection (pg. 11, para. 2 – pg. 12, para. 1). Applicant references the Declaration under 37 CFR 1.132 (hereinafter “Declaration”), and argues that the COVIDSeq Test Pipeline has little speed cost, reduces processing time, and improves speed and accuracy of SARS-CoV-2 detection (pg. 12, para. 2-4). Applicant’s argument is not persuasive because:
Based upon Declaration para. 6, the improvements are conferred by the k-mer algorithm of the COVIDSeq Test Pipeline. Regarding claim 1, the k-mer algorithm appears to refer to limitations of counting first and second k-mers and determining that the first and second k-mers are above respective thresholds. However, these limitations recite a judicial exception. MPEP 2106.05(a) recites “the judicial exception alone cannot provide the improvement.”
Furthermore, the claims do not reflect the improvement. Improvements derived from the COVIDSeq Test Pipeline are directed toward detecting SARS-CoV-2 as well as splitting sequencing reads in to 32-mers. However, claims 1, 12 and 21 do not recite these limitations. MPEP 2106.05(a) recites “the claim must be evaluated to ensure the claim itself reflects the disclosed improvement in technology … That is, the claim must include the components or steps of the invention that provide the improvement described in the specification.”
Applicant argues improvement in computer efficiency when reciting “improves the computing efficiency of detection”, “computational efficiency improvement over conventional analysis” and “reduction in the computational resources per sample” (pg. 12, para. 5 – last para.) (pg. 13, para. 2). Applicant’s argument is not persuasive because:
MPEP 2106.05(a)(I) recites “in order for a method claim to improve computer functionality, the broadest reasonable interpretation of the claim must be limited to computer implementation.” Claims 1 and 12 are not computer-implemented and thus would not improve computer technology.
Claim 21 is computer-implemented. However, the computer itself has not been altered in any way, i.e., by changing the functioning of a processor or by changing the way in which it stores or accesses memory. Nothing about the physical components of the computer nor the way the computer operates is changed. Applicant has not provided any evidence or technical explanation for how the claimed invention improves the way in which the asserted abstract idea improves the way in which the computer processes or stores data. Rather, the computer is presented with less data (i.e. fewer sequencing reads) for downstream analysis, which inherently requires fewer computing resources.
Applicant argues that the k-mer algorithm allows efficient diversion of only positive samples for downstream analysis which improves computational efficiency (pg. 12, last para.). Applicant’s argument is not persuasive because:
This improvement appears to refer to claim 1 limitations of “providing a positive detection output” and “initiating sequence alignment”. However, these limitations recite a judicial exception. The judicial exception alone cannot provide the improvement (MPEP 2106.05(a)).
Applicant’s remarks regarding the Declaration providing evidence for improvements in sequencing technology are not persuasive for the same reasons discussed in responses above (pg. 13, para. 4-5).
Response to Subject Matter Eligibility Declaration
The Declaration under 37 CFR 1.132 (hereinafter “Declaration”) filed 04/01/2026 is insufficient to overcome the rejection of claims 1-2, 7, 10-12, 15 and 21-22 under 35 USC 101 for being directed to an abstract idea without significantly more as set forth in the last Office action because:
Declaration para. 5-7 argue improvement in speed, accuracy and detection of SARS-CoV-2 RNA using COVIDSeq Test Pipeline as recited in para. 3-4. Applicant’s arguments are not persuasive because:
Based upon Declaration para. 6-7, the improvements are conferred by the k-mer algorithm of the COVIDSeq Test Pipeline. Regarding claim 1, the k-mer algorithm refers to limitations of counting first and second k-mers and determining that the first and second k-mers are above respective thresholds. These limitations recite a judicial exception. MPEP 2106.05(a) recites “the judicial exception alone cannot provide the improvement.”
Furthermore, the claims do not reflect the improvement. Improvements derived from the COVIDSeq Test Pipeline are directed toward detecting SARS-CoV-2 as well as splitting sequencing reads in to 32-mers. However, claims 1, 12 and 21 do not recite these limitations. MPEP 2106.05(a) recites “the claim must be evaluated to ensure the claim itself reflects the disclosed improvement in technology … That is, the claim must include the components or steps of the invention that provide the improvement described in the specification.”
Declaration claims improvement in computer efficiency in para. 8-9. Applicant’s argument is not persuasive because:
MPEP 2106.05(a)(I) recites “in order for a method claim to improve computer functionality, the broadest reasonable interpretation of the claim must be limited to computer implementation.” Claims 1 and 12 are not computer-implemented and thus would not improve computer technology.
Claim 21 is computer-implemented. However, the computer itself has not been altered in any way, i.e., by changing the functioning of a processor or by changing the way in which it stores or accesses memory. Nothing about the physical components of the computer nor the way the computer operates is changed. Applicant has not provided any evidence or technical explanation for how the claimed invention improves the way in which the asserted abstract idea improves the way in which the computer processes or stores data. Rather, the computer is presented with less data (i.e. fewer sequencing reads) for downstream analysis, which inherently requires fewer computing resources.
In view of the foregoing, when all of the evidence is considered, the totality of the rebuttal evidence of nonobviousness fails to outweigh the evidence of obviousness.
Conclusion
No claims are allowed.
Claims 1-2, 7, 10-12, 15 and 21-22 are free from the prior art because the prior art does not fairly teach or suggest in claims 1, 12 and 21 counting k-mers from sequencing reads using a first hash table initialized with k-mers of a pathogen genome and a second hash table initialized with human control k-mers, wherein k-mer counts from each hash table must be above a respective threshold to generate a positive detection output which is used to either terminate counting k-mers (claim 1), terminate analysis of sequence data (claim 12), or initiate sequence alignment of only positive detection output samples (claim 21).
The closest prior art is Panyukov et al. (“Panyukov”; International Journal of Molecular Sciences 21, no. 3 (2020): 944; previously cited on PTO892 mailed 10/01/2025) and Wu et al. (“Wu”; US 2019/0172553 A1; previously cited on PTO892 mailed 10/01/2025).
Panyukov uses unique k-mers as strain-specific barcodes for phylogenetic analysis and natural microbiome profiling using hash tables (abstract) (sec. 4.3). Panyukov recites “we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn’s disease” (abstract).
Wu discloses quality control metrics for sequencing reads which includes identification of one or more species from which the reads were generated using k-mers and hash tables (abstract) [14] [70]. Wu teaches terminating sequencing in real-time based on quality metrics [89].
However, Panyukov in view of Wu does not render prima facie obvious counting k-mers using separate hash tables (one for pathogens and one for human control), comparing the k-mer counts to respective thresholds, and determining a positive pathogen detection for each sample based on both thresholds being exceeded, wherein the positive detection is then used to terminate counting k-mers in real-time as samples are actively sequenced, terminate sequence data analysis, or initiating sequence alignment.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Noah A. Auger whose telephone number is (703)756-4518. The examiner can normally be reached M-F 7:30-4:30 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
Prosecution Insights