Prosecution Insights
Last updated: April 19, 2026
Application No. 17/092,975

BACTERIAL CAPTURE SEQUENCING PLATFORM AND METHODS OF DESIGNING, CONSTRUCTING AND USING

Final Rejection §101§103
Filed
Nov 09, 2020
Examiner
LIU, GUOZHEN
Art Unit
1686
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
The Trustees of Columbia University in the City of New York
OA Round
4 (Final)
50%
Grant Probability
Moderate
5-6
OA Rounds
4y 8m
To Grant
75%
With Interview

Examiner Intelligence

Grants 50% of resolved cases
50%
Career Allow Rate
47 granted / 95 resolved
-10.5% vs TC avg
Strong +25% interview lift
Without
With
+25.4%
Interview Lift
resolved cases with interview
Typical timeline
4y 8m
Avg Prosecution
39 currently pending
Career history
134
Total Applications
across all art units

Statute-Specific Performance

§101
37.1%
-2.9% vs TC avg
§103
25.2%
-14.8% vs TC avg
§102
7.3%
-32.7% vs TC avg
§112
19.8%
-20.2% vs TC avg
Black line = Tech Center average estimate • Based on career data from 95 resolved cases

Office Action

§101 §103
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's Amendment/Request for Reconsideration-After Non-Final Rejection, filed 9 October 2025, has been entered and fully considered Status of Claims Claims 7-8, 13-14, 17-28, 32, 34, 37-43 and 45-59 are cancelled. Claims 1-6, 9-12, 15-16, 29-31, 33, 35-36 and 44 are pending and are examined on the merits. Priority Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/675,890, filed 05/24/2018 is acknowledged Withdrawn Rejections/Objections The rejections to claim 1 under 35 U.S.C. 112(a) in the Office action mailed 11 August 2025 is withdrawn in view of claim amendments filed 9 October 2025. The rejections to claims 1-6, 9-12, 15-16, 29-31, 33, 35-36 and 44 under 35 U.S.C. 112(b) in the Office action mailed 11 August 2025 is withdrawn in view of claim amendments filed 9 October 2025. Claim Rejections - 35 USC § 101 This rejection is newly installed. The rejection is necessitated by claim amendments. 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. Claim 1 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. Step 1: Process, Machine, Manufacture or Composition Claim 1 is to a non-transitory computer readable medium, so a machine. Step 2A Prong One: Identification of Abstract Ideas The claim recites: b) extracting and pooling coding sequences from the nucleotide sequences obtained in a); --This step is interpreted as extracting and pooling coding sequences from one or more bacteria sequence. This process can be accomplished in human mind with the help of a pen and paper. Therefore, this step equates to an abstract idea of mental processes. c) breaking the coding sequences into fragments, wherein the fragments are about 50 to about 100 nucleotides in length and are tiled across the coding sequences at specific intervals to obtain sequence information to design oligonucleotides that selectively hybridize to genomes of pathogenic bacteria; and --This step is interpreted as breaking down a big sequence fragment into small consecutive pieces. This process can be accomplished in human mind with the help of a pen and paper. Therefore, this step equates to an abstract idea of mental processes. d) providing the bacterial capture sequencing platform or design thereof, wherein the bacterial capture sequencing platform includes oligonucleotides designed based on the obtained sequence information to selectively hybridize to genomes of pathogenic bacteria --This step is to provide a design, which reads on activities in human mind. Therefore, this step equates to an abstract idea of mental processes. Step 2A Prong Two: Consideration of Practical Application The claims result in a process of providing the bacterial capture sequencing platform or design thereof, which reads on activities in human mind and is to an abstract idea of mental processes. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application. This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria: An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field; an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition; an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim; an additional element effects a transformation or reduction of a particular article to a different state or thing; and an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception. Step 2B: Consideration of Additional Elements and Significantly More The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to: A non-transitory computer readable medium. Obtaining nucleotide sequences of at least one bacteria listed. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because obtaining bacteria sequence data is an insignificant extra-solution activity of gettering data. The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of data gathering. Other elements of the method include “a non-transitory computer readable medium”, which is a recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter. Claim Rejections - 35 USC § 103 This rejection is maintained from the previous Office Action. 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, 4-6, 9-12, 15-16, 29-31, 33, 35-36 and 44 are rejected under 35 U.S.C. 103 as being unpatentable over Bent et al. ("Enriching pathogen transcripts from infected samples: a capture-based approach to enhanced host–pathogen RNA sequencing." Analytical Biochemistry 438.1 (2013): 90-96. Cited on the 2/28/2025 IDS), Briese ("Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis." MBio 6.5 (2015): 10-1128. Previously cited), and Brandon (“Microbial Markers and Uses Therefor”, US 20160145696 A1, Date Published 2016-05-26. Cited on the 11/9/2020 IDS), Claim 1 is interpreted as a software product (disk) for designing and constructing a bacterial capture platform using oligonucleotides. Claim 1 provides the designed end product in the form of a “capture sequencing platform” wherein the platform can be a cleavable microarray (claim 11), while the sequencing part is not claimed in claim 1. Under a BRI, claim 1 is interpreted as a target enriching design which targeting the infectious bacteria. Regarding Claim 1, Bent teaches a method of designing and/or constructing a pathogen that include bacteria capture sequencing platform comprising oligonucleotides for the simultaneous detection, identification and/or characterization of pathogenic bacteria (Section “Abstract”, pg. 90) and Bent provides “The reads passing the quality filter were then aligned to individual RVFV strain MP-12 segments or the F. tularensis subsp. Holarctica LVS genome using Geneious software 6.0.3 [22]. In addition, F. tularensis reads were aligned to the proper genome by Bowtie 2, and FPKM (fragments per kilobase per million mapped reads) values were calculated for each gene using Cufflinks”, which is implicit for a non-transitory computer executable media and software instructions. Further, Bent teaches acquiring the bacteria Francisella tularensis nucleic acids (3rd para., col 1, page 91 through 3rd para., col 2, page 91). Brandon teaches the detection, identification and/or characterization of pathogenic bacteria ([21-22]). Briese provides “Toward this end, oligonucleotides were selected to represent all viral taxa containing at least one virus known to infect vertebrates; virus families that include exclusively viruses infecting plants or insects were excluded (see Table S1 in the supplemental material). Coding sequences were extracted from the EMBL Coding Domain Sequence database, clustered at 96% sequence identity (page 1, col 2, last para), which teaches extracting and pooling coding sequences in platform design. Bent does not teach in silico sequence extracting and pooling. Briese provides “a set of 342,438 coding sequence records was identified for the selected virus genera. The sequences were broken into fragments, clustered at 90% sequence identity, and used to generate 100-nt probe sequences that were tiled across the genes at approximately 25- to 50-nt intervals” (last para lines 10-14, col 2, pg. 7), which teaches the oligonucleotide array design that breaking coding sequences into fragments. Bent does not teach in silico sequence extracting and pooling. Briese provides “a library of 1,993,200 oligonucleotide probes was selected. The NimbleGen cleavable array platform was employed for synthesis of the biotinylated, soluble probe library (SeqCap EZ Choice; Roche/NimbleGen, Basel, Switzerland), and probe sequences were refined by adjusting their lengths to conform to NimbleGen synthesis parameters, such as maximum Tm or homopolymer repeat length” (last para line 14, col 2, pg. 7 through 1st para, col 1, pg. 8), which teaches the outputting the of the designed oligonucleotide array. Claim 9 is interpreted as the “method” version for the software disk version of claim 1. The art applied to claim 1 also teach claim 9. Regarding claim 4, Briese provides “The final library comprised 1,993,176 oligonucleotides ranging in length from 50 to 100 nt and in Tm from 58.7°C to 101°C” (1st para last 3 lines, col 1, pg. 2), which teaches the melting temperature for the oligo design that overlap the range in the instant claim 4. Regarding claim 5, Briese provides “Where technical complexity in oligonucleotide synthesis was challenging due to melting temperature (Tm) or homopolymer repeats, probe sequences were refined by shortening and adjusting their start/stop positions. The final library comprised 1,993,176 oligonucleotides ranging in length from 50 to 100 nt and in Tm from 58.7°C to 101°C” (1st para last lines 4-10, col 1, pg. 2), which teaches the melting temperature for the oligo design that overlap the range in the instant claim 5. Regarding claim 6, Briese provides “The final library comprised 1,993,176 oligonucleotides ranging in length from 50 to 100 nt and in Tm from 58.7°C to 101°C” (1st para last 3 lines, col 1, pg. 2), which suggest an average length for the oligo designed to be around 75 nt. Regarding claim 10, Briese provides “A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform” (Section Abstract, lines 5-6, pg. 1), which teaches the nucleotide acids array. Regarding claim 11, Briese provides “A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform” (Section Abstract, lines 5-6, pg. 1), which teaches the nucleotide acids array is synthesized on a cleavable platform. Regarding claim 12, Briese provides “A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform” (Section Abstract, lines 5-6, pg. 1), which teaches the nucleotide acids array is synthesized on a cleavable platform binding to the biotin support. Regarding claim 15, Briese provides “A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform” (Section Abstract, lines 5-6, pg. 1), which teaches the nucleotide acids array is in the form of a oligonucleotide library. Regarding claim 16, Briese provides “A biotinylated oligonucleotide library was synthesized on the NimbleGen cleavable array platform” (Section Abstract, lines 5-6, pg. 1), which teaches the nucleotide acids array is synthesized on a cleavable platform. Regarding claim 29, Briese teaches a method of detecting the presence of bacteria in a sample through capture sequencing comprising oligonucleotides hybridization capture for the simultaneous detection, identification and/or characterization of pathogenic virus nucleic acids isolated from samples (Section Abstract, pg. 90). Brandon teaches the detection, identification and/or characterization of pathogenic bacteria ([21-22]). Regarding claim 30, Brandon teaches the sample can be chosen from the group consisting of a biological sample, a food sample, and other environmental samples ([41]) . Regarding claim 31, Brandon teaches the sample is biological samples selected from among blood, tissue, sputum, lavage fluid, feces, urine and saliva ([41]). Regarding claim 33, Brandon teaches the subject is human ([41]). Regarding claim 35, Briese provides “a set of 342,438 coding sequence records was identified for the selected virus genera. The sequences were broken into fragments, clustered at 90% sequence identity, and used to generate 100-nt probe sequences that were tiled across the genes at approximately 25- to 50-nt intervals” (last para lines 10-14, col 2, pg. 7), which teaches the oligonucleotide array design. Regarding claim 36, Bent teaches a method of detecting the presence of bacteria in a sample through capture sequencing comprising oligonucleotides hybridization capture for the simultaneous detection, identification and/or characterization of pathogenic bacteria nucleic acids isolated from samples (Section Abstract, pg. 90). Brandon teaches the detection, identification and/or characterization of pathogenic bacteria ([21-22]). Regarding claim 44, Bent teaches a method of detecting the presence of bacteria in a sample through capture sequencing comprising oligonucleotides hybridization capture for the simultaneous detection, identification and/or characterization of pathogenic bacteria nucleic acids isolated from samples (Section Abstract, pg. 90). Brandon also teaches the detection, identification and/or characterization of pathogenic bacteria ([21-22]). It would have been prima facie obvious to modify Bent’s pathogen capture sequencing platform design which target both virus and bacteria (Section Abstract, page 90), with Briese’s method in high throughput design of virus capture sequencing platform using oligonucleotides, and Brandon’s teaching of bacteria detection, identification and/or characterization (Brandon: para [21-22]), because high through-put identification and characterization of bacteria is urgently needed (Brandon: para [3-5]). One would reasonably expect success for the modification because Bent already succeed in capturing sequencing both virus and bacteria in one platform (Bent: “By creating probes to the entire viral or bacterial genome using an inexpensive and unbiased process, we are able to produce a sufficient amount of probes not only to capture a dynamic range of transcripts but also to capture any RNA species that may be expressed by the pathogen. In addition, the probe generation process is simple and flexible, allowing for the rapid production of probes to any pathogen of interest“ (1st para., col 2, page 95), and Briese and Brandon, like Bent, are all about microbial detection and identification. Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Bent, Briese and Brandon, as discussed above over claims 1, 4-6, 9-12, 15-16, 29-31, 33, 35-36 and 44, and in view of Jia ("CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database." Nucleic acids research (2016): gkw1004. Newly cited). Bent in view of Briese and Brandon teach a bacterial capture sequencing platform design and construction using oligonucleotides, and identification and characterization of bacteria use the same, as discussed above over claims 1, 4-6, 9-12, 15-16, 29-31, 33, 35-36 and 44. Regarding claim 2, Bent in view of Briese and Brandon does not teach the CARD database. Jia teaches the CARD database. Jia further teaches the use of CARD in design and gene sequence identification (“Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence” (Jia: Section Abstract, pg. D566). It would have been prima facie obvious to modify the bacteria sequence collections in the combined Bent’s, Briese’s and Brandon’s design of a capture sequencing platform using oligonucleotides targeting bacteria, with Jia’s teaching of the CARD database, (Jia: Section Abstract, pg. D566), because the CARD database will allow high through-put design related to the bacteria antibiotic resistance genes (Jia: Section Abstract, pg. D566). One would reasonably expect success for the modification because Jia’s CARD already collected and verified the antibiotic resistance genes which will save time. Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Bent, Briese and Brandon, as discussed above over claims 1, 4-6, 9-12, 15-16, 29-31, 33, 35-36 and 44, and in view of Chen ("VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors." Nucleic acids research 40.D1 (2012): D641-D645. Newly cited). Briese in view of Brandon teach a bacterial capture sequencing platform design and construction using oligonucleotides, and identification and characterization of bacteria use the same, as discussed above over claims 1, 4-6, 9-12, 15-16, 29-31, 33, 35-36 and 44. Regarding claim 3, Bent in view of Briese and Brandon does not teach the VFDB database. Chen teaches the VFRD database. It would have been prima facie obvious to modify the virus sequence collections in the combined Bent’s, Briese’s and Brandon’s design of a capture sequencing platform using oligonucleotides targeting bacteria, with Chen’s teaching of the VFDB database (Chen: Title and Section Abstract, pg. D641), because the VFDB database will allow for high through-put design related to bacteria virulence factor sequence. One would reasonably expect success for the modification because Chen’s virulence factor database “has provided the broadest and most comprehensive up-to-date information regarding experimentally validated bacterial virulence factors (e.g. extracellular products, such as enzymes and toxins and secreted effectors or cell-associated products, such as capsular polysaccharides and outer membrane proteins), and has further explored plasticity in the repertoire of VFs on an intra-genera level since its second release (Chen: 2nd para lines 1-10, col 2, pg. D641). Response to Applicant’s Argument In the Remarks filed 9 October 2025, Applicant argues (page 26, 2nd para) that “applicant submits that Bent differs from the claimed invention at least in that it is completely silent with regard to the design of a capture sequencing platform capable of simultaneously detecting, identifying, and/or characterizing pathogenic bacterial species. Rather, Bent relates to capture-based enrichment and sequencing analysis of a single bacterial species (i.e., Francisella tularensis induced to infect a mouse macrophage like cell line in vitro).” To response, this argument is not persuasive. Claims 1 and 9 preamble and step 1 read as (emphasis added): “A non-transitory computer readable medium including computer readable instructions that when executed by a computer causes the computer to carry out a method of designing and/or constructing a bacterial capture sequencing platform comprising oligonucleotides for the simultaneous detection, identification and/or characterization of pathogenic bacteria known or suspected to infect vertebrates and antimicrobial resistant genes or biomarkers, the steps comprising: a) obtaining nucleotide sequences of at least one bacteria listed as follows:” According to the Remarks (page 23, last para through page 24, 1st para), "A and/or B" covers embodiments having element A alone, element B alone, or elements A and B taken together. Claims 1 and 9 do not require all the bacteria species listed. The claims only require one bacteria from the list since the recite “at least one bacteria.” Therefore, Bent reference is encompassed by the instant limitation of claim 1. Bent teaches a method of designing and constructing a pathogen that include bacteria capture sequencing platform comprising oligonucleotides for the simultaneous detection, identification and characterization of pathogenic bacteria (Section Abstract, pg. 90). Therefore, the Bent reference is also encompassed by the claim limitation “designing and/or constructing a bacterial capture sequencing platform comprising oligonucleotides for the simultaneous detection, identification and/or characterization of pathogenic bacteria”. In the Remarks, Applicant argues (page 26, last para) that: “Bent does not teach a method of designing and/or constructing a bacteria capture sequencing platform comprising oligonucleotides for the simultaneous detection, identification and/or characterization of pathogenic bacteria as alleged by the Examiner, but merely performs a low scale approach to detect F. tularensis from an artificially infected mouse cell line.” To response, the argument is not persuasive. In response to applicant's arguments against the references individually, one cannot show nonobviousness by arguing against references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). It is noted that the rejection of claim 1 is based on a combination of the Bent, Briese and Brandon. Briese teaches the large-scale platform design. In the Remarks, Applicant further argues (page 27 through page 28, 1st para) that Briese’s teaching in virus capture sequencing platform does not make it obvious for bacteria capture sequencing platform. Although infectious bacteria and virus are usually studied and handled by the by the same group of people in the universities as well as in the hospitals, and reagents of isolating bacteria nucleic acids and virus nucleic acids are commercial available. The inventors of the current invention admitted (Allicock, Orchid M., et al. "BacCapSeq: a platform for diagnosis and characterization of bacterial infections." MBio 9.5 (2018): 10-1128. Newly cited. Pages 1, last line through page 2, first 2 lines) that “Here, we describe a bacterial capture sequence system, BacCapSeq, modeled on VirCapSeq-VERT, an analogous system developed to detect all known viruses infecting vertebrates (10).” Therefore Applicant’s argument is not persuasive again. In the Remarks, Applicant argues (page 28, 2nd para) that: “The increased number of coding sequences present in bacteria, which is further augmented by sequences encoding antimicrobial resistant biomarkers and virulence factors, and would have understood that such an increase could significantly impact the number of oligonucleotides needed to specifically, accurately, and simultaneously detect all the bacterial species present in a complex sample, but that the number of oligonucleotides would also be limited by imposing physical restraints on the platform itself (e.g., a high number (~5 X 10⁶) of oligonucleotides increasing viscosity of the platform to the point that it is no longer useful).” To respond, the inventors of the current invention admitted (Allicock, Orchid M., et al. "BacCapSeq: a platform for diagnosis and characterization of bacterial infections." MBio 9.5 (2018): 10-1128. Newly cited. Pages 1, last line through page 2, first 2 lines) that “Here, we describe a bacterial capture sequence system, BacCapSeq, modeled on VirCapSeq-VERT, an analogous system developed to detect all known viruses infecting vertebrates (10).” Bent teaches (page 90, Section “Abstract”) a capture-based approach to capture both virus and bacteria in one platform and Bent stressed that “this versatile method can, in principle, enrich for any pathogen in any infected sample. Therefore Applicant’s argument is not persuasive again. The arguments related to complexity and viscosity is not supported by evidence. Illumina demonstrated that the whole human genomes can be put in one microarray design. The commercial product was available before the filing date of instant invention. Illumina’s commercial products proofed that complexity and viscosity are not a problem. In the Remarks, Applicant argues (page 28, last para through page 29, 1st para) that Branda’s 16S rRNA is a low-resolution approach. This argument is not supported by evidence. Briese does teach in silico pooling and extracting nucleotide sequence for a in silico design. In the Remarks, Applicant argues (page 29, 2nd para) that: “Bent's approach based on the teachings of Briese and Brandon fails to recognize the context of these unrelated teachings and the unpredictability associated with simultaneous identification and/or characterization of pathogenic bacteria using a single bacterial capture sequencing platform. Although Bent was able to individually capture one RVFV virus using an RVFV specific platform and one F. tularensis bacterial strain using a total genomic DNA-derived F. tularensis specific platform, this low scale single plex detection approach combined with the teachings of Briese (whose viral platform is built upon and detects a fundamentally different class of sequences) and Brandon (who used a completely different low resolution 16S rRNA SNP classification approach), would not have provided a POSA with any reasonable expectation of successfully arriving at the claimed invention.” In response, Applicant’s arguments are not persuasive. Instant claims requires only a single bacteria for the capture platform design. On the other hand, Bent’s method of capture-based approach demonstrated capturing both virus and bacteria in one platform and Bent stressed that “this versatile method can, in principle, enrich for any pathogen in any infected sample (Bent: Section “Abstract”, pg. 90). Argument over 16S rRNA SNP is not supported by evidence. In the Remarks, Applicant argues (page 29, penultimate para) that Jia and Chen do not overcome the shortcomings in prior art. To response, Applicant’s argument is not persuasive. Jia and Chen are introduced for the purpose of the CARD database and the VFDB database. Briese taught the design principle and major steps for the capture sequencing platform targeting infectious virus and Bent demonstrated that capture sequencing both virus and bacteria in one platform is possible. Bent shows that Briese’s teaching is combinable. Hence the 103 rejection is maintained. Conclusion No claims are 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. Any inquiry concerning this communication or earlier communications from the examiner should be directed to GUOZHEN LIU whose telephone number is (571)272-0224. The examiner can normally be reached Monday-Friday 8-5. 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, Larry D Riggs can be reached at (571) 270-3062. 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. /GL/ Patent Examiner Art Unit 1686 /Anna Skibinsky/ Primary Examiner, AU 1635
Read full office action

Prosecution Timeline

Nov 09, 2020
Application Filed
Jul 14, 2024
Non-Final Rejection — §101, §103
Dec 16, 2024
Response Filed
Apr 04, 2025
Final Rejection — §101, §103
Jun 30, 2025
Response after Non-Final Action
Jul 31, 2025
Non-Final Rejection — §101, §103
Oct 09, 2025
Response Filed
Jan 21, 2026
Final Rejection — §101, §103
Apr 16, 2026
Interview Requested

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Prosecution Projections

5-6
Expected OA Rounds
50%
Grant Probability
75%
With Interview (+25.4%)
4y 8m
Median Time to Grant
High
PTA Risk
Based on 95 resolved cases by this examiner. Grant probability derived from career allow rate.

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