DETAILED ACTION
Applicant’s response, filed 02 Oct. 2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Any references to Applicant’s specification are with respect to the originally filed copy, filed 19 Feb. 2020.
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 .
Status of Claims
Claims 2, 6-15, and 24-28 are cancelled.
Claims 1, 3-5, and 16-23 are pending.
Claims 1, 3-5, and 16-23 are rejected.
Priority
The effective filing date of the claimed invention is 28 Feb. 2019.
Claim Interpretation
Claim 1 recites “…producing, using a sequencing system, a plurality of sequence reads… wherein:…. each sequence read in the plurality of sequence reads comprises a corresponding plurality of single-pass subreads derived from the corresponding genomic fragment; each respective sequence read in the plurality of sequence reads is a single molecule consensus sequence (SMCS) in a plurality of SMCS, and each respective SMCS in the plurality of SMCSs comprises a sub-plurality of subreads…”. Applicant’s specification at FIG. 1 discloses the SMCS is generated based on alignment of subreads. Therefore, the step of producing a plurality of sequencing reads requires both physically generating reads (i.e. the single-pass subreads derived from the corresponding genomic fragment) using a sequencer and also analyzing the subreads to form each sequence read that is a single molecule consensus sequence (SMCS).
Claim 1 recites a “homopolymer-collapsed sequence (HCS)”. The term “homopolymer-collapsed sequence” is defined at para. [0044] of the specification to be a sequence derived from a parent sequence in which each instance of multiple consecutive identical nucleotides in a parent sequence is replaced by a single nucleotide of the same type, and provides the example that ATGCG is the homopolymer collapsed sequence of AATGGGCCG. Therefore, the term will be interpreted accordingly.
Claim 1 recites “…identifying/identify one or more connected components in the overlap graph…”. In light of Applicant’s specification at para. [0100], a connected component of the overlap graph is interpreted to refer to two or more vertices connected by one or more edges in the overlap graph.
Claim 22 recites “…a first and second genomic loci having high sequence similarity…”. In light of Applicant’s specification at para. [0048], sequences sharing a high sequence similarity are interpreted to refer to sequences with a sequence similarity such that the differences between the sequences are not readily detectable.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 12 and 23-24 under 35 U.S.C. 112(b) in the Office action mailed 02 June 2025 has been withdrawn in view of claim amendments and cancellations received 02 Oct. 2025.
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.
Claims 17-18 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. This rejection is newly recited and necessitated by claim amendment.
Claims 17-18 are indefinite for recitation of “the genomic sample”. There is insufficient antecedent basis for this limitation in the claim because claim 1, from which claims 17-18 ultimately depend, do not recite a genomic sample. For purpose of examination, the limitation is interpreted to refer to a genomic sample from which the genomic fragments were obtained.
Response to Arguments
Applicant’s remarks at pg. 7, para. 8 regarding 35 U.S.C. 112(b) have been fully considered but they do not pertain to the new grounds of rejection set forth above.
Claim Rejections - 35 USC § 101
The rejection of claim 24 under 35 U.S.C. 101 in the Office action mailed 02 June 2025 has been withdrawn in view of the cancelation of this claim received 02 Oct. 2025.
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 3-5, and 16-23 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Any newly recited portion herein is necessitated by claim amendment.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claim 1 being representative) is directed a method for assembling a genome or chromosome. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim 1 recites the following steps which fall under the mental processes groupings of abstract ideas:
…a plurality of sequence reads… wherein: the plurality of sequence reads collectively comprise a plurality of indel errors, each genomic fragment in the plurality of genomic fragments is 10 kb or longer, each sequence read in the plurality of sequence reads comprises a corresponding plurality of single-pass subreads derived from the corresponding genomic fragment, each respective sequence read in the plurality of sequence reads is a single molecule consensus sequence (SMCS) in a plurality of SMCS generated from the plurality of single-pass subreads, and each respective SMCS in the plurality of SMCSs comprises a sub-plurality of subreads in the corresponding plurality of single-pass subreads of a corresponding genomic fragment in the plurality of genomic fragments;
generating… for each sequence read in the plurality of sequence reads, a homopolymer-collapsed sequence (HCS) and a corresponding homopolymer encoded sequence (HES), thereby generating a plurality of HCS reads and a plurality of HES reads;
generating…a plurality of pairs of HCS reads by performing exact string matching of the plurality of HCS reads, where each pair of HCS reads differs only by one or more homopolymer indels and exactly matches in their homopolymer-collapsed forms over a contiguous length of at least 0.5 kb, such that the exact string matches identify sequence reads that originate from the same genomic fragment;
generating….an overlap graph from the plurality of HCS reads, wherein the overlap graph comprises a plurality of vertices and a plurality of directed edges, each vertex of the graph representing an HCS read in the plurality of HCS reads and each directed edge in the plurality of directed edges connecting from a first vertex to a second vertex whenever the HCS reads corresponding to the first and second vertices are determined, based on the identified exact string matches, to originate from the same genomic fragment;
identifying…one or more connected components in the directed overlap graph;
generating… a multiple sequence alignment for each connected component in the one or more connected components, thereby generating one or more multiple sequence alignments;
generating…a homopolymer-collapsed consensus sequence by concatenating a basecall at each aligned position in a first multiple sequence alignment in the one or more multiple sequence alignments;
determining…a plurality of vector data structures, wherein each respective data structure in the plurality of vector data structures corresponds to a position in the homopolymer-collapsed consensus sequence, and wherein
(i) a number of elements in each respective vector data structure equals the number of HCS reads covering the corresponding position in the homopolymer-collapsed consensus sequence; (ii) each respective element of each respective vector data structure in the plurality of vector data structures is associated with an HCS read, in the number of HCS reads, covering the position, ((iii) each respective element of each respective vector data structure in the plurality of vector data structures is further associated with a corresponding HES read, in the plurality of HES reads, and (iv) each respective element of each respective vector data structure in the plurality of vector data structures stores a homopolymer length in the respective position in the HES read.
assigning… for each respective position in the homopolymer-collapsed consensus sequence, a corresponding consensus homopolymer length to the respective position using a floor of a median of the number of elements in the respective data structure corresponding to the respective position.
replacing… each position in the homopolymer-collapsed consensus sequence with a homopolymer string formed by N successive copies of a nucleotide at that position, wherein N is the assigned corresponding consensus homopolymer length calculated for that position, to generate a homopolymer-expanded consensus sequence, thereby assembling the genome or chromosome.
The identified claim limitations fall into one of the groups of abstract ideas of mental processes for the following reasons. First, obtaining sequence reads comprising indel errors that are single molecule consensus sequences by combining a plurality of subreads can be practically performed in the mind by taking the most abundant nucleotide at each position across the subreads to generate a single consensus read. Generating a HCS and corresponding HES for each sequence read can be performed mentally by analyzing a read to identify any homopolymer runs, and replacing the homopolymer run with a single base at each position of the run (e.g. AATCCG -> ATCG). Furthermore, generating a plurality of suffix/prefix exact string matches as claimed for the HCS reads involves performing data comparisons to identify a match of least 0.5 kb between a suffix of one HCS and a prefix of another HCS (e.g. ATCGA with CGATC), which is a mental process. Generating an overlap graph from the plurality of HCS reads can be performed mentally aided with pen and paper by analyzing the suffix/prefix exact string matches for the HCS reads and drawing an edge between each pair of HCS reads that contain a suffix/prefix exact string match. Identifying one or more connected components in the overlap graph involves identifying a sequence of nodes in the graph that are continuously connected by edges, which can be performed mentally. The step of generating a multiple sequence alignment for each connected component can be performed mentally by comparing the sequences corresponding to the one or more connected components (i.e. the sequences of the HCS reads) to identify a continuous alignment in the sequences corresponding to the nodes in the connected component. Next, generating a homopolymer-collapsed consensus sequence by concatenating the base calls at each aligned position in one of the multiple sequence alignments involves analyzing the multiple sequence alignment and connecting together the base calls at each position, which is a mental process. Furthermore, determining a vector of homopolymer lengths for each position as claimed in the homopolymer-collapsed consensus sequence can be performed mentally by counting a number of HCS reads corresponding to each position, creating a vector the length of the number of HCS reads for each position, and then analyzing the HES reads for each HCS and assigning the number of homopolymers in each HCS read at the respective position to the respective vector. Assigning a consensus homopolymer length for each position in the homopolymer-collapsed consensus sequence can be performed mentally by selecting the most recurrent homopolymer length in each vector (i.e. selecting the homopolymer length by majority vote). Replacing each position in the homopolymer-collapsed consensus sequence with a homopolymer string formed by N successive copies of a nucleotide at that position involves decompressing the homopolymer collapsed sequence reads to determine the full consensus sequence (e.g. ATCG back to AATCCG). Overall, other than reciting the steps are carried out by a processor, nothing in the claims precludes the above steps from being practically performed in the mind and thus the limitations recite a mental process. See MPEP 2106.04(a)(2) III.
Additionally, using a floor of a median of the number of elements in the respective vector to assign a homopolymer length further recites a mathematical concept. See MPEP 2106.04(a)(2) I.
Dependent claims 3-5, 16-17, and 19-23 further recite an abstract idea and/or further limit the abstract idea of claim 1. Dependent claims 3-5 further limit the mental process of generating suffix/prefix exact string matches to be of a minimum length of 0.5 kb to 10 kb, 5 kb to 8 kb, or 6 kb to 7kb, respectively. Dependent claim 16 further limits the mental process of assembling a genome or chromosome to be for a human genome or chromosome. Dependent claim 17 further limits the mental process of claim 17 to involve repeating the above mental process steps of claim 1 for different genomes. Dependent claim 19 further recites the mental process of placing HCSs that are not in the one or more connected components into a holding bin and verifying variant calls using one or more HCS in the holding bin. Dependent claim 20 further recites the mental process of pre-selecting sequence reads from an initial set of sequence reads that map to one or more genomic regions of interest. Dependent claim 21 further recites the mental process of performing a sequence similarity search and pre-selecting reads from an initial set including a first sequence read mapping to each of a first and second genomic region of interest in the plurality of genomic regions. Dependent claim 22 further limits the mental process of pre-selecting sequence reads of claim 20 to be from an initial set of sequence reads that map to one or more genomic regions comprising first and second genomic loci having a high sequence similarity. Dependent claim 23 further recites the mental process of generating separate consensus sequences for the first and second genomic loci. Therefore, claims 1, 3-5, and 16-23 recite an abstract idea. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Claims 3-5, 16, and 19-23 further recite a mental process and/or are further limit the mental process, as discussed above, but to do not recite any elements in addition to the recited judicial exception, and thus are part of the judicial exception.
The additional elements of claim 1 include:
a computer system;
producing, using a sequencing system, a plurality of sequence reads through continuous sequencing of a plurality of circular sequencing templates, wherein each circular sequencing template comprises:
(i) a double-stranded insert region corresponding to a genomic fragment in a plurality of overlapping genomic fragments representing the genome or the chromosome;
(ii) a first hairpin adapter covalently linking the 3' end of one strand of the insert to the 5' end of the complementary strand; and
(iii) a second hairpin adapter covalently linking the 5' end of the one strand of the insert to the 3' end of the complementary strand,
wherein:…the plurality of sequence reads collective comprise a plurality of indel errors; each genomic fragment in the plurality of genomic fragments is 10 kb or longer;
outputting the homopolymer-expanded consensus sequence, thereby assembling the genome or chromosome (i.e. outputting data).
The additional elements of claims 17-18 include:
wherein the genomic sample comprises multiple different genomes (claim 17); and
wherein the genomic sample is a metagenomic sample comprising multiple microbial genomes (claim 18).
The additional elements of a computer system and outputting data are generic computer components. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Furthermore, the additional element of outputting the homopolymer-expanded consensus sequence, only serves to output the information generated by the abstract idea, which also amounts to insignificant extra-solution activity that does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
With respect to the additional elements relating to producing the sequence reads, as claimed, the additional elements only serve to collect the necessary information for use by the abstract idea (i.e. sequencing reads for assembly), which similarly amounts to insignificant extra-solution activity that does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g). The additional elements of claims 17-18 only further limit the sequencing to be of particular genomes, which is part of the insignificant extra-solution activity of claim 1.
Furthermore, the additional elements (i)-(iii) relating to the circular sequencing templates, this only serves to generally link the use of the judicial exception to particular technological environment of single molecule real time sequencing, specifically SMRTBELL®, as described in Applicant’s specification pertaining to the circular templates (see FIG. 1). The additional elements of claims 17-18 only further limit the genomic samples being sequenced, and thus also serve to generally link the use of the judicial exception to the technological environment of microbiomes or metagenomics. See MPEP 2106.05(h), stating limitations that amount to merely indicating a field of use or technological environment in which to apply a judicial exception cannot integrate a judicial exception into a practical application.
Therefore, the additionally recited elements amount to insignificant extra-solution activity, merely invoke computers as a tool to perform the abstract idea, and/or merely indicate a technological environment in which to apply a judicial exception, and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1, 3-5, and 16-23 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception for the following reasons.
Claims 3-5, 16, and 19-23 further recite a mental process and/or are further limit the mental process, as discussed above, but to do not recite any elements in addition to the recited judicial exception, and thus are part of the judicial exception.
The additional elements of claim 1 include:
a computer system;
producing, using a sequencing system, a plurality of sequence reads through continuous sequencing of a plurality of circular sequencing templates, wherein each circular sequencing template comprises:
(i) a double-stranded insert region corresponding to a genomic fragment in a plurality of overlapping genomic fragments representing the genome or the chromosome;
(ii) a first hairpin adapter covalently linking the 3' end of one strand of the insert to the 5' end of the complementary strand; and
(iii) a second hairpin adapter covalently linking the 5' end of the one strand of the insert to the 3' end of the complementary strand,
wherein:…the plurality of sequence reads collective comprise a plurality of indel errors; each genomic fragment in the plurality of genomic fragments is 10 kb or longer;
outputting the homopolymer-expanded consensus sequence, thereby assembling the genome or chromosome (i.e. outputting data).
The additional elements of claims 17-18 include:
wherein the genomic sample comprises multiple different genomes (claim 17); and
wherein the genomic sample is a metagenomic sample comprising multiple microbial genomes (claim 18).
The additional elements of a computer system and outputting data are conventional computer components. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
The additional elements of sequencing reads through continuous sequencing of a plurality of circular sequencing templates, as recited in claim 1, in addition to sequencing a metagenomic sample comprising multiple genomes (claims 17-18), are well-understood, routine, and conventional. This position is supported by Slatko et al. (Overview of Next-Generation Sequencing Technologies, 2018, Current Protocols in Molecular Biology, e59, pg. 1-11; newly cited), Applicant’s own specification, and Maccannell (Platforms and Analytical Tools Used in Nucleic Acid Sequence-Based Microbial Genotyping Procedures, 8 Feb 2019, Microbial Spectrum, 7(1), pg. 1-17; newly cited).
Slatko reviews next-generation sequencing technologies, and discusses “third” generation sequencing technologies, or large fragment single molecule sequencing, and that the current commercialized technology leader in this area is Pacific Biosciences (PacBio), which has commercialized single molecule real time (SMRT) sequencing, enabling very long fragments up to 30 to 50kb to be sequenced (i.e. 10kb or longer fragments are sequenced) (pg. 5, col. 1, para. 3). Slatko then explains template preparation is unique in the PacBio process, as it involves production of a “SMRTbell”, a circular double-stranded DNA molecule with a known adapter sequence complementary to the primers used to initiate the DNA synthesis on the template, which enables the polymerase to read through large templates numerous times by traversing the circular molecule until the polymerase stops to build up a circular consensus sequence (pg. 5, col. 2, para. 1-2). Slatko also explains PacBio SMRT sequencing suffers from an inherently high error rate (pg. 6, col. 1, para. 2), and that using PacBio technology, it is straightforward to assemble a complete bacterial genome sequence (pg. 66, col. 1, para. 3). Applicant’s specification at para. [0018] and FIG. 1 also overviews PacBio’s SMRTBELL polynucleotide substrate (a double-stranded polynucleotide with hairpin adapters). Therefore, the additional elements for generating the sequencing reads using a sequencing system are well-understood, routine, and conventional.
Furthermore, Maccannel reviews sequencing platforms for microbial genotyping procedures (Abstract), and discloses that PacBio instruments perform single-molecule, real-time (SMRT) sequencing, which has become increasingly useful for deep sequencing and metagenomic applications (pg. 10, col. 2, para. 1), and the longer read lengths produced by PacBio are an important advantage in the phasing and assembly of metagenomics samples (i.e. samples containing multiple genomes) (pg. 11, col. 2, para. 2). Therefore, even considering the additional elements in combination, producing the sequencing reads on metagenomic samples using PacBio SMRT sequencing is well-understood, routine, and conventional.
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 02 Oct. 2025 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks that claim 1 recites “producing, using a sequencing system, a plurality of sequence reads through continuous sequencing of a plurality of circular sequencing templates…”, and these features produce long sequencing reads that include indel errors arising from the circular template structure, and such reads are unconventional and differ substantially from typical short-read next generation sequencing reads, and the technical problem addressed by the claimed invention in assembling genomes from long, indel-prone reads (Applicant’s remarks at pg. 8, para. 2-4).
This argument is not persuasive. While Applicant alleges the sequencing data used in the claim is “unconventional”, this is not the case, as demonstrated by Slatko and Maccannel in the above rejection. The claims merely use conventional PacBio SMRT sequencing to generate long reads. For example, each of Slatko (pg. 66, col. 1, para. 3) and Maccannel (pg. 11, col. 2, para. 2) discuss the advantages of using SMRT sequencing in sequencing assembly due to their long reads, and Slatko further notes that PacBio SMRT sequencing suffers from an inherently high error rate (pg. 6, col. 1, para. 2)
Regarding Applicant’s argument that the claim addresses the technical problem in assembling genomes from long reads, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. See the discussion of Diamond v. Diehr, 450 U.S. 175, 187 and 191-92, 209 USPQ 1, 10 (1981)) in subsection II, below. In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception. Furthermore, it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. See MPEP 2106.05(a).
In the instant case, the alleged improvement in assembling genomes (or chromosomes as claimed) from long, indel-prone reads is an improvement in the abstract idea itself, rather than a technology. As noted above, the additional elements relating to producing the sequencing reads merely utilize conventional SMRT sequencing to generate the reads for assembly, and any alleged improvement is derived from the abstract idea alone of generating the homopolymer collapsed consensus reads and ultimately the homopolymer-expanded consensus sequence.
Applicant remarks the claimed HCS/HES transformations and exact string matching provide a technical solution, and the combination of transformations and exact string matching is specifically designed to overcome limitations inherent in the claimed circular sequencing templates (Applicant’s remarks at pg. 8, para. 5 to pg. 9, para. 2). Applicant further remarks the HCS/HES constructs and associated vector data structures allow a computer to systematically and efficiently handle the massive sequencing datasets associated with assembling a genome, providing a practical and technical solution to a real-world problem, and for instance, the HCS/HES constructs allow for exact string matching sequencing, which allows for the assembly of a genome using the error prone sequence reads associated with circular sequencing templates (Applicant’s remarks at pg. 9, para. 2).
This argument is not persuasive. As discussed above, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements or by the additional element(s) in combination with the recited judicial exception. Furthermore, it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology. See MPEP 2106.05(a).
The combination of transformations, including generating HCS, generating HES, performing exact string matching, constructing vector data structures (e.g. <1, 4, 5, 7, 6>), and generating a homopolymer-expanded censuses sequence are part of the abstract idea, and therefore cannot provide the improvement alone. Overall, the alleged improvement amounts to an improvement in the abstract idea (i.e. the analysis of the sequencing reads) rather than a technology.
While Applicant alleges the HCS/HES constructs and associated vector data structures “allow a computer to systematically and efficiently handle the massive sequencing datasets”, in computer-related technologies, the examiner should determine whether the claim purports to improve computer capabilities or, instead, invokes computers merely as a tool. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016). MPEP 2106.05(a) further explains, during examination, the examiner should analyze the "improvements" consideration by evaluating the specification and the claims to ensure that a technical explanation of the asserted improvement is present in the specification…Generally, examiners are not expected to make a qualitative judgement on the merits of the asserted improvement.
In the instant case, it is not clear how a HCS or HES and simple vectors of data are improving computer capabilities. Arguments of counsel alone cannot take the place of evidence in the record. Instead, it appears that any more efficient handling of data is merely the result of an improved data analysis being carried out on a computer, which is not an improvement to computer technology as set forth above.
Applicant remarks the claimed invention cannot be performed mentally because 1) each circular sequencing template generates numerous long reads requiring subread analysis; 2) exact string matching of HCS reads over lengths of 0.5kb across the millions of reads necessary to encode a genome or chromosome cannot be performed by humans without computational assistance; 3) generating and manipulating vector data structures is computationally intensive and impractical manually, particularly at the scale of genomes or chromosomes; and 4) the reconstruction of homopolymer-expanded consensus sequences from HES vectors the scale of chromosomes relies on systemic computation to resolve overlapping reads, and therefore the claimed processes require a computer to execute, and the scale and complexity of the data precludes any practical mental performance (Applicant’s remarks at pg. 9, para. 3 to pg. 10, para. 2).
This argument is not persuasive. First, the arguments are not commensurate with the scope of the claims. Claim 1 does not require any particular number of sequence reads, such as “millions of reads”, and instead encompasses generating thousands of reads to assemble a small 130,000 base pair chromosome.
Furthermore, the amount of data, in and of itself is not a limitation which takes a process out of the realm of the human mind. It is the process performed on that data which is the mental step, and mental steps identified in the claims do not have to be fastest, most efficient, or require specialized computing elements. The various limitations relating to performing a subread consensus analysis, exact string matching (i.e. comparing two sequences), generating and analyzing vector data structures, and reconstructing the homopolymer-expanded consensus sequence can all be performed in the human mind for the reasons discussed in the above rejection, albeit very slowly, using pen and pencil, and slightly faster using the general purpose computer as a tool or in a computing environment. While, computations on large amounts of data performed mentally, or with paper and pencil, would take considerable time and effort, the singular purpose of computers and computer networks is to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general-purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also SiRF Tech., Inc. v. Int’l Trade Comm ’n, (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations).
Applicant remarks the claimed computer elements provide significantly more than a generic computer because (1) the computer elements are configured to perform a specifical technological solution of operating on novel HCS/HES data structures, including exact string matching, generating vectors, and reconstructing homopolymer-expanded sequences, (2) the operations cannot be performed manually or with conventional methods on the scale of genomes or chromosomes, and (3) the exact string matching allows computational alignment at speeds and inaccuracy impossible at the scale of genomes or chromosomes without the claimed computer configuration, thereby improving genome assembly (Applicant’s remarks at pg. 10, para. 2).
This argument is not persuasive. In computer-related technologies, the examiner should determine whether the claim purports to improve computer capabilities or, instead, invokes computers merely as a tool. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016). See MPEP 2106.05(a). In the instant case, regarding (1), claim 1 merely performs the various abstract idea steps “using a computer system”, which merely invokes computers as a tool as already discussed above. Regarding (2), this argument is not persuasive for the reasons discussed above regarding why the limitations recite a mental process. Last, regarding (3) an improvement in the abstract idea itself is not an improvement to technology, as discussed above.
Applicant remarks the claims integrate the judicial exception into a practical application because each step is directed to a specific technical solution to a technical problem: the accurate assembly of genomes from long, indel-prone reads, and integrates the claimed processes into a practical technological application (Applicant’s remarks at pg. 10, para. 3 to pg. 11, para. 2).
This argument is not persuasive for the reasons already discussed above. Overall, the alleged improvement of increasing accuracy in read assembly through exact string matching using “error-free” HCSs, amounts to an improved analysis of sequence reads, which is an improvement in the abstract idea, rather than technology.
Conclusion
No claims are allowed.
Claims 1, 3-5, and 16-23 are free of the prior art for the reasons discussed in the Office action mailed 05 May 2023.
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
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685