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 .
Applicant Response
Applicant's response, filed 09/16/2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Claim Status
Claims 10 is canceled.
Claims 1-9 and 11-20 are pending and under examination herein.
Claims 1-9 and 11-20 are rejected.
Priority
The instant application is a Continuation of 16776405 , filed 01/29/2020 , which is a continuation of 15917286 , filed 03/09/2018 ,which is a continuation of PCT/US2016/052912 , filed 09/21/2016, which claims the benefit of priority from US Provisional Application 62/221574 , filed 09/21/2015. As such, the effective filing date assigned to each of claims 1-9 and 11-20 is 09/21/2015.
Drawings
The objections to the drawings are withdrawn in view of amendments to the specification filed 09/16/2025.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 7-8 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 and necessitated by claim amendments.
Claims 7 and 8 recites the limitation "the first alignment" in line 2, respectively. There is insufficient antecedent basis for this limitation in the claim, as claims 1 and 6, on which claims 7-8 are dependent on, do not recite a first alignment.
Claim Rejections - 35 USC § 101
The rejection of claim 10 under 35 U.S.C. 101 is withdrawn in view of cancelation of the claim in the claim amendments filed 09/16/2025.
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 1-9 and 11-20 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Newly recited portions are necessitated by claim amendments.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 1 recites for each of the matching reference genomes: based at least in part on the initial alignment results, identifying an optimally-aligning sequence read that aligns to the matching reference genome with an optimal alignment score, thereby obtaining optimally- aligning sequence reads; providing the matching reference genomes.
Claim 6 recites further comprising determining whether any of the new alignment scores exceeds the optimal alignment score for the optimally-aligning sequence read.
Claim 7 recites further comprising removing the matching reference genome of the first alignment from the matching reference genomes when one new alignment score of the plurality of new alignment scores exceeds the optimal alignment score for the optimally-aligning sequence read.
Claim 12 recites further comprising identifying a set of the sequence reads that aligned to two or more of the reference genomes with at a least a minimum alignment threshold.
Claim 13 recites further comprising, for each sequence read of the set of the sequence reads, identifying two or more matching reference genomes of the reference genomes to which the sequence read aligns with at least the minimum alignment threshold.
Claim 14 recites further comprising assigning a taxonomy identifier from the classification information to each of the two or more of the reference genomes, thereby obtaining assigned taxonomy identifiers, each taxonomy identifier including at least two levels of classification, the at least two levels having a hierarchy such that there is a lower level and at least one higher level.
Claim 15 recites further comprising comparing the assigned taxonomy identifiers of the two or more reference genomes at each of the at least two levels of classification.
Claim 16 recites further comprising removing each level of the at least two levels from the assigned taxonomy identifiers that do not match between the two or more reference genomes.
Claim 17 recites further comprising assigning to the sequence read a lowest level of the at least two levels of the assigned taxonomy identifiers that is shared between the two or more reference genomes.
Claim 18 recites further comprising providing an identification of one or more taxonomy identifiers corresponding to one or more candidate pathogens based on numbers of corresponding sequence reads assigned to each of the plurality of taxonomy identifiers.
Claim 19 recites further comprising associating an unassigned state with the sequence read when none of the at least two levels of the taxonomy identifiers match.
These recitations equate to steps of collecting information, analyzing data and making observations, evaluations and judgements that can be carried out in the human mind. Specifically, identifying an optimally-aligning sequence with an optimal alignment score, comparing scores to other scores, removing genomes from a set based on scores or sharing the same taxonomic level as a reference genome corresponding to a score, assigning and comparing taxonomy identifies or states, and providing matching reference genomes or results can be practically performing the human mind as claimed and are similar to the concepts of collecting and comparing known information in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1067, 100 USPQ2d 1492, 1500 (Fed. Cir. 2011) and collecting information, analyzing it, and reporting certain results of the collection and analysis in Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016) that the courts have identified as concepts that can be practically performed in the human mind. Therefore, each of the above recited limitations fall under the “Mental Processes” grouping of abstract ideas. Claims 4, 6 and 20 further qualify the recited judicial exceptions. As such, claims 1-9 and 11-20 recite an abstract idea (Step 2A, Prong 1: YES).
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). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere data-gathering and insignificant extra-solution activity, and mere instructions to perform an abstract idea on a generic computer:
Claim 1 recites sequencing deoxyribonucleic acid (DNA} molecules derived from a sample of biological material to produce a plurality of sequence reads, the sample comprising DNA molecules or ribonucleic acid (RNA) molecules from a plurality of organisms;(b) using a global nucleotide alignment technique to align the plurality of sequence reads to a plurality of reference genomes, thereby obtaining initial alignment results that include, for each of at least a portion of the plurality of sequence reads, a matching reference genome to which the sequence read aligns; (d) for each of the optimally-aligning sequence reads: applying a local nucleotide alignment technique for the optimally-aligning sequence read to the plurality of reference genomes, thereby obtaining second alignment results, wherein the global nucleotide alignment technique and the local nucleotide alignment technique are different.
Claim 2 recites wherein the DNA comprises complementary DNA (cDNA).
Claim 3 recites wherein the cDNA is derived from RNA in the sample.
Claim 11 recites wherein the initial or the second alignment results include classification information for each of the matching reference genomes, the classification information including a plurality of taxonomy identifiers.
Claims 1-3 and 11 recite limitations for gathering data and on the type of data gathered. The alignment steps are performed to gather data to perform the mental steps, and there is no indication that these steps are impacted by the recited the judicial exception, and therefore the recited judicial exception is not integrated into these additional elements. These limitations equate to mere data gathering and selecting a particular data source or type of data to be manipulated, and data outputting, which the courts have found to be insignificant extra-solution activity (see MPEP 2106.05(g)).
The claims also recite using a generic computing systems and computer program products to carry out instructions to implement an abstract idea on a computer, as the method is computer-implemented. There are no limitations that indicate that the claimed steps require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. Furthermore, 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 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).
There is no indication that any of these additional elements provide a practical application of the recited judicial exception outside of the judicial exception itself. As such, claims 1-9 and 11-20 are directed to an abstract idea (Step 2A, Prong 2: NO).
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). Further analyzing the additional elements under step 2B, the additional elements as described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims under the 2B analysis, receiving sequence data and performing aligning are laboratory techniques that the courts have recognized as well-understood, routine, conventional activity in the life science arts, as they are similar to using polymerase chain reaction to amplify and detect DNA (Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) and Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015)), amplifying and sequencing nucleic acid sequences (University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)) and analyzing DNA to provide sequence information or detect allelic variants (Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546. (See MPEP2106.05(d)). Furthermore the prior art to Naccache et al. (IDS 03/25/2025, NPL ref 7 and supplemental materials, p 1-74; previously cited) and Huson et al. ((IDS 03/25/2025, NPL ref 7; previously cited), discloses performing next-generation sequencing of nucleic acids (DNA, RNA, cDNA) and receiving sequence reads (Naccache et al.: abstract; fig 1; supplemental material, p 4- 6; Supplemental table S4; Huson et al.: abstract; p 377, col 2, para 2; fig 1).
Furthermore, the prior art to Thompson et al. (Bioinformatics, Volume 19, Issue 9, June 2003, Pages 1155–1161; previously cited) discloses a program for two-step refinement process by determining and aligning global and then local core blocks, in which well aligned regions can be differentiated and alignment correction is then restricted to the less reliable regions and the error correction stage involves a hierarchical, progressive realignment of the local regions defined in the initial analysis stage (abstract; p 1156, col 2, para 3- p 157, col 2, para 6). The prior art to Homer et al. (BMC Bioinformatics 2009, 10, 175, pages 1-11; previously cited) also discloses local sequence alignment is typically a final finishing step in a two-stage search process found in many current sequence alignment tools that support alignment of a short sequence to an entire genome (p 2, col 1, para 2). Chaisson and Tesler ( BMC Bioinformatics 2012, 13, 238; previously cited) also discloses aligning SMS reads with high indel rates to genomes as follows: first, find clusters of short exact matches between the read and the genome using either a suffix array or BWT-FM index, and then, perform a more detailed alignment of the regions where reads are matched to assign the alignment (p 2, col 1, para 4-p 3, col 1, para 1; fig 9). Lindahl et al. (New phytologist 199(1), pp.288-299; previously cited) reviews analysis of high-throughput sequencing of amplified marker in fungal communities, and discloses Global alignment also enables analysis of the phylogenetic distance between communities, using tools such as UniFrac, in which the difference between communities depends not only on which members are included, but also on how closely related they are (p 294, col 2, para 2). Schneeberger et al. (Genome Biol 2009, 10, R98; p 1-12; newly cited), discloses a publicly available software tool, GenomeMapper, which supports simultaneous mapping of short reads against multiple genomes and performs both accurate global and local alignments, and that with the first step of the alignment procedure, GenomeMapper scans the hash index for k-mers identical between read and genome graph to detect quickly all genomes and locations with nearly identical alignments, in the second step, GenomeMapper determines the location and sequence of nearly identical maximal substrings (NIMS) between read and genome graph, and finally, GenomeMapper will perform a k-banded alignment by applying dynamic programming to ensure a consistent gap placement (abstract; fig 1; p 2, col 2, para 1-2; p 5, col 1, para 4-p 6, col 1, para 3; fig 1-2; p 11, col 1, para 2). The prior at to Swei et al. (PloS one, 8(4), p.e62083, p 1-9; newly cited) also discloses extracting cNDA and using SNAP and then BLASTn to perform both global and local alignments for a plurality of reference genomes (p 5, col 1, para 2-col 2, para 2; table 1).
As such, activities such as data gathering do not provide a non-conventional or unconventional step. Rather, the data gathering and outputting steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Therefore, the additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception, and the claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-9 and 11-20 are not patent eligible.
Response to applicant’s arguments
Applicant states the claims recites elements that are not practical to be performed in the mind, at least because these elements necessitate performing DNA sequencing as well as using both a global and local alignment technique to align sequence reads to reference genomes (Applicant’s Arguments, p 7, para 7 – p 8, para 1).
It is respectfully submitted that this is not persuasive. As discussed in MPEP 2106.04(I)(A), Step 2A is a two-prong inquiry, in which examiners determine in Prong One whether a claim recites a judicial exception. In other words, Step 2A, Prong 1 simply evaluates whether the claim recites any judicial exceptions, and the absence or presence of additional elements which are not judicial exceptions, such as sequencing and aligning sequence reads to reference genomes, do not influence the evaluation. If any judicial exceptions are found to be recited by the claim under the analysis under Step 2A, Prong 1, the analysis then moves to Step 2A, Prong 2. And, as discussed above, the claims were found to recite judicial exceptions under Step 2A, Prong 1.
Applicant states the claim 1 are patent-eligible because it provides a specific inventive concept, as it recites elements rooted in computer technology that when considered as an ordered combination, are routinely performed by those if skill in the art, and none of the cited art discloses the combination of the additional elements of claim 1, steps a, b, and d, as the prior at to Naccache et al., Huson et al. and Lindahl do not discloses the use of a global and local nucleotide alignment technique, Thompson et al. does not disclosed identifying an optimally-aligning sequence read and applying a local nucleotide alignment technique for the optimally-aligning sequence read to the plurality of reference genome, and Homer et al. and Chaisson et al. do not disclose applying the alignment techniques to a plurality of genomes (Applicant’s Arguments, p 8, para 2 – p 12, para 2).
It is respectfully submitted that this is not persuasive. As discussed above, the prior art to Thompson et al. (Bioinformatics, Volume 19, Issue 9, June 2003, Pages 1155–1161; previously cited) discloses a program for two-step refinement process by determining and aligning global and then local core blocks (abstract; p 1156, col 2, para 3- p 157, col 2, para 6). Schneeberger et al. (Genome Biol 2009, 10, R98; p 1-12; newly cited), discloses a publicly available software tool, GenomeMapper, which supports simultaneous mapping of short reads against multiple genomes and performs both accurate global and local alignments, and that with the first step of the alignment procedure, GenomeMapper scans the hash index for k-mers identical between read and genome graph to detect quickly all genomes and locations with nearly identical alignments, in the second step, GenomeMapper determines the location and sequence of nearly identical maximal substrings (NIMS) between read and genome graph, and finally, GenomeMapper will perform a k-banded alignment by applying dynamic programming to ensure a consistent gap placement (abstract; fig 1; p 2, col 2, para 1-2; p 5, col 1, para 4-p 6, col 1, para 3; fig 1-2; p 11, col 1, para 2). The prior at to Swei et al. (PloS one, 8(4), p.e62083, p 1-9; newly cited) also discloses extracting cNDA and using SNAP and then BLASTn to perform both global and local alignments for a plurality of reference genomes (p 5, col 1, para 2-col 2, para 2; table 1).
Therefore, the additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception, and the claims do not amount to significantly more than the judicial exception itself. As such, the claims are not patent eligible.
Claim Rejections - 35 USC § 103
The rejection of claim 10 under 35 U.S.C. 103 is withdrawn in view of cancelation of the claim in the claim amendments filed 09/16/2025.
The rejection of claims 1-20 under 35 U.S.C. 103 as being unpatentable over Naccache et al. (IDS 03/25/2025, NPL ref 7 and supplemental materials p 1-74; hereafter referred to as Naccache), as evidenced by Ye et al. (BMC Bioinformatics 2011, 12, 159; hereafter referred to as Ye), in view of Huson et al. (IDS 03/25/2025, NPL ref 7), is withdrawn in view of claim amendments filed 09/16/2025 and in view of Applicant Argument’s filed 09/16/2023, stating that the cited prior art does not recite the amended claim 1 limitations of applying both a global and local alignment technique for the sequence reads to the plurality of reference genomes, as RAPSearch used by Naccache is a protein similarity tool, and the cited art to Huson and Ye also do not teach this (Applicant’s Arguments, p 12, para 4 – p 14, para 3).
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-9 and 11-20 are rejected under 35 U.S.C. 103 as being unpatentable over Naccache et al. (IDS 03/25/2025, NPL ref 7 and supplemental materials p 1-74; hereafter referred to as Naccache; previously cited), in view of Huson et al. (IDS 03/25/2025, NPL ref 7; previously cited) and Swei et al. (PloS one, 8(4), p.e62083, p 1-9; newly cited; hereafter referred to as Swei). This rejection is newly recited and necessitated by claim amendments.
With respect to claims 1, 9 and 20, Naccache discloses a cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples, and performing alignment with alignment thresholds to reference genomic sequences using two sequential alignment techniques, SNAP and then RAPSearch , and performing a preliminary subtraction of sequence reads that align to a human genome using SNAP (title; fig 1; p 1182-1191).
Naccache discloses performing sequencing numerous serum, stool, tissue, CSF, Cell line, lung swab samples from different patients, and that these samples included viruses and bacteria (supp materials, p 5, para 2-p 8, para 3).
Naccache also discloses removal of low quality and low complexity scores, and removing reads that remained in figure 1 and page 1190. Naccache discloses performing the initial SNAP alignment, then performing de novo assembly for those reads that remained unclassified combined with reads identified as viral, and duplicate reads, and then performing translated nucleotide (protein) alignment, indicating the second alignment technique would also be applied for all optimal-aligning sequence reads (fig 1; supp materials, p 12, para 2). Naccache further discloses reporting a list of all classified reads with taxonomic assignments, a summary table of read counts, and both viral and bacterial genomic coverage maps (fig 1). Naccache discloses SNAP is a global aligner and that the secondary alignment aligner was RAPSearch alignment (fig 1; supp materials, p 3, para 1). The instant specification discloses SNAP and RAPSearch are global aligners and BLASTn is a local aligner (para 00134).
However, Naccache does not appear to disclose also using a local alignment technique for the optimally aligning sequence reads.
However, the prior at to Swei, in the same field of endeavor, discloses extracting cNDA and using SNAP/RAPSearch and then BLAST to perform both global and local alignments for a plurality of reference genomes (p 5, col 1, para 2-col 2, para 2; table 1). Swei specifies, preprocessed reads were then analyzed using a rapid computational pipeline incorporating the SNAP and RAPSearch aligners for alignment to nucleotide and protein databases, respectively, to identify viral sequences, and candidate viral sequences were subsequently confirmed as true by direct BLASTn alignment to the identified viral genus or species using an E-value cutoff of 1×10−8 (p 5, col 2, para 2). Swei further discloses for these initial alignments, the advantage of SNAP and RAPSearch was a 10–1,000X increase in computational speed while maintaining comparable accuracy relative to existing algorithms such as BLASTn/BLASTx (p 5, col 2, para 2).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the alignment method using SNAP and RAPSearch of Naccache by adding a step of performing a local alignment on the candidate sequences as disclosed by Swei, as the advantage of SNAP and RAPSearch was a 10–1,000X increase in computational speed while maintaining comparable accuracy relative to existing algorithms such as BLASTn/BLASTx, and using BLASTn on the candidate viral sequences provides confirmation. There is a reasonable expectation of success, as applying a confirmatory local alignment technique would not impede the method of Naccache, as Naccache also discloses that the gold standard criterion for a correct viral classification was BLASTn alignment against the target viral genome (p 1190, col 1, para 3).
With respect to claims 2 and 3, Naccache discloses using cDNA derived from RNA (supp. Materials, p 6, para 2).
With respect to claims 11, 18 and 20, Naccache discloses reads are aligned using SNAP to all nucleotide sequences in the NCBI nt collection, enabling identification of bacteria, fungi, parasites, and viruses, indicating reads would comprise taxonomic identifiers (fig 1). Naccache discloses the reference genomes include taxonomy identifiers which are outputs of results of a single taxonomy classification for the sample (fig 5; fig 7).
However, with respect to claims 1 and 4-7, Naccache does not appear to disclose alignment scores or removing matches based on the score. With respect to claims 8, 13-17 and 19, Naccache also does not appear to disclose removing the matching reference genome when it shares a same taxonomic level as a reference genome corresponding to the new alignment scores or show consideration of multiple taxonomy identifiers and assigning a sequence read to the lowest shared level.
However, with respect to claims 1 and 4-7, the prior art to Huson, in the same field of endeavor, discloses a process of aligning sequence reads from a metagenomics sample to genomic databases to identify the organisms present in the sample (MEGAN) (abstract). Huson further discloses using a bit-score threshold of 100 for alignment and retaining only those hits whose bit scores lie within 5% of the best score, indicating that reads (and therefore the matching genome) would be removed base on the moving scale of the what constitutes a best score (p 379, col 1, para 2-p 383, col 2, para 5; p 385, col 2, para 2-3).
With respect to claims 8, 13-17 and 19, Huson further discloses a process of determining the lowest common ancestor (termed LCA) for a sequence read (which is the lowest shared level) by analyzing alignments to reference genome (abstract; fig 2; p 385, col 2, para 3-5). Huson also discloses discarding genomes with unassigned reads (p 383, col 2, para 1)
Huson further discloses sequence comparisons are computationally intensive and time-consuming, they should be performed only once with sufficiently relaxed alignment parameters, and MEGAN provides filters to adjust the level of stringency (p 383, col 2 para 5).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the process of Naccache by removing alignments that have a lower score from either alignment protocol to retain the best alignments to indicate the most likely taxonomic classifier for a sample. It would have been further obvious to select the lowest shared taxonomic classifier because Huson et al. provides guidance to select the lowest common ancestor when aligning sequence reads from a complex sample to reference genomes as the best indication of the taxonomic classifier for the sample. Although Naccache does not disclose scoring of alignments, it would have been obvious to use the scoring of alignments of Huson to determine which reference genome has the best matches to sequence reads of a sample, because sequence comparisons are computationally intensive and time-consuming, they should be performed only once with sufficiently relaxed alignment parameters, and the methods of Huson provides filters to adjust the level of stringency, as disclosed by Huson.
Therefore, the invention is prima facie obvious.
Response to applicant’s arguments
Applicant states the cited prior art does not recite the amended claim 1 limitations of applying both a global and local alignment technique for the sequence reads to the plurality of reference genomes, as RAPSearch used by Naccache is a protein similarity tool, and the cited art to Huson and Ye also do not teach this (Applicant’s Arguments, p 12, para 4 – p 14, para 3).
It is respectfully submitted that this is not persuasive. Applicant’s arguments have been fully considered, and the prior art to Swei has been newly cited to teach these limitations, as discussed above.
Double Patenting
The rejection of claim 10 on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US11380421B2 is withdrawn in view of cancelation of the claim in the claim amendments filed 09/16/2025.
The rejection of claim 10 on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. US11515006B2 is withdrawn in view of cancelation of the claim in the claim amendments filed 09/16/2025.
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-9 and 11-20 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US11380421B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the claim limitations of U.S. Patent No. US11380421B2 are narrower in scope than those of the instant claims, and therefore anticipate the limitations of the instant claims.
Claims 1-9 and 11-20 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. US11515006B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the claim limitations of U.S. Patent No. US11380421B2 are narrower in scope than those of the instant claims, and therefore anticipate the limitations of the instant claims.
Response to applicant’s arguments
Applicant states the instant claim 1 has been amended to clarify the claimed subject matter, and therefore the instant claims are patentably distinct from claims 1-12 of the ‘421 patent and claims 1-15 of the ‘006 patent and requests withdrawal of the non-statutory double patenting rejections (Applicant’s Arguments, p 15, para 1-4).
It is respectfully submitted that this is not persuasive, as the reference patents disclose the amended limitations of instant claim 1.
With respect to instant claim 1, the reference patent ‘421 discloses “sequencing of sequencing DNA molecules from the sample of biological material” in claim 9, and “using an initial global alignment technique to align the population of sequence reads to a plurality of classified reference genomes in an electronic database” and applying a second local alignment technique for the optimally-aligning sequence read to the classified reference genomes in claim 1.
Reference patent ‘ 006 discloses “sequencing DNA molecules from the sample of biological material” in claim 11, “using a first alignment technique to align the plurality of sequence reads to a plurality of classified reference genomes in a database” and “applying a second alignment technique for the optimally-aligning sequence read to the classified reference genomes” in claims 1 and 12, and “ wherein the initial alignment technique uses a global alignment algorithm and the second alignment technique uses a local alignment algorithm” in claim 15.
Therefore, the non-statutory double patenting rejections are maintained.
Conclusion
No claims allowed.
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.
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/N.D./Examiner, Art Unit 1686
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687