DETAILED ACTION
Comments
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . 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.
Claims 1-3, 5-7, 24, 33, 42, 49, 56, 60-61, 65-66, 69-71, 128, and 130 are pending and examined in the instant Office action.
Information Disclosure Statement
The IDS filed on 8/17/2022 has been considered.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
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 5, 56, and 69-71 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.
Claim 5 recites that an oncogenic pathogen is an oncogenic virus listed in Table 1. For the purpose of clarity, the relevant oncogenic viruses from Table 1 should be incorporated into the text of claim 5.
Claim 56 recites that probes collectively represent at least four of the portions of viral genomes listed in Table 2. For the purpose of clarity, the relevant portions of viral genomes listed in Table 2 should be incorporated into the text of claim 56.
Claim 69 recites that the plurality of genes includes at least five genes listed in Table 21. For the purpose of clarity, the relevant genes from Table 21 should be incorporated into the text of claim 69.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim(s) 1-3, 5-7, 24, 33, 42, 49, 56, 60-61, 65-66, 69-71, 128, and 130 is/are 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. Claims 1-3, 5-7, 24, 33, 42, 49, 56, 60-61, 65-66, and 69-71 are drawn to methods, claims 128 is drawn to a non-transitory computer-readable storage medium, and claim 130 is drawn to a system comprising a processor.
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:
The independent claims recite the mental step of obtaining data regarding sequence reads pertinent to a sample from a subject.
The independent claims recite the mental steps of determining whether each sequence read aligns to a sequence on a human reference genome or whether each sequence read algins to a reference genome of an oncogenic pathogen.
The independent claims recite the mental step of tracking the cumulative number of reads aligning with human versus pathogen sequences.
The independent claims recite the mental step of using this sequence count to determine whether a subject is afflicted with an oncogenic pathogen.
Claim 2 recites the mental step of constraining the oncogenic pathogen to be an oncogenic virus.
Claims 3 and 7 recite the mental steps of determining that the subject has cancer, and determining, based on gene maps, the strain of cancer obtained by the subject.
Claim 5 recites the mental step of constraining the oncogenic pathogen to be an oncogenic virus listed in Table 1.
Claim 6 recites the mental step of constraining the oncogenic pathogens to be a member of a virus family.
Claim 24 recites the mental step of constraining the plurality of human genomic loci to comprise at least 100 human genomic loci.
Claim 33 recites the mental steps of constraining the plurality of sequence reads to have an average length of at least 50 nucleotides and wherein the plurality of sequence reads comprises 25 million sequence reads.
Claim 42 recites the mental steps of using hash tables wherein the seed length is at least 16 nucleotides in length.
Claim 49 recites the mental step of constraining the blood sample to comprises blood or saliva.
Claim 56 recites the mental step of constraining the portions of viral genomes to be the portions listed in Table 2.
Claims 60-61 and 65-66 recite the mental steps of generating reports containing the diagnosis, cancer data, the strain of pathogens, and treatment recommendations.
Claim 69 recite the mental steps of obtaining the genetic data and then applying the genetic data to a trained classifier to discriminate as to whether the subject has HPV related cancer or HPV-free cancer.
Claim 70 recites the mental step of constraining the cancer to be cervical cancer.
Claim 71 recites the mental step of constraining the cancer condition to be head and neck cancer.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-3, 5-7, 24, 33, 42, 49, 56, 60-61, 65-66, 69-71, 128, and 130 recite(s) an abstract idea/law of nature/natural phenomenon (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 instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment.
While claim 66 recommends therapies, there is no active limitation of treating the subject with a particular therapy.
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. As such, claims 1-3, 5-7, 24, 33, 42, 49, 56, 60-61, 65-66, 69-71, 128, and 130 is/are directed to an abstract idea/law of nature/natural phenomenon (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). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
The document of Pyeon et al. [WO 2017/070709A1] teaches that obtaining biological samples from a subject, performing hybridization, and alignment of sequence reads are routine and conventional in the prior art.
As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. 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. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-3, 5-7, 24, 33, 42, 49, 56, 60-61, 65-66, 69-71, 128, and 130 is/are not patent eligible.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-2, 5-6, 24, 33, 49, 60-61, 65, 128, and 130 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lo et al. [US PGPUB 2018/0208999 A1; on IDS].
Claim 1 is directed to a method of determining whether a subject is afflicted with an oncogenic pathogen.
The method comprises obtaining an amount of nucleic acid from a biological sample of the subject. The amount of nucleic acid comprises nucleic acid from the subject and potentially nucleic acid from at least one oncogenic pathogen in a plurality of oncogenic pathogens. [Claim 1 of Lo et al. teaches obtaining a sample from a subject comprising nucleic acid from a subject and potentially nucleic acid from a pathogen.]
The method comprises hybridizing the amount of nucleic acid to a probe set. The prove set includes a plurality of nucleic acid probes for a plurality of human genomic loci and a respective set of nucleic acid probes for a corresponding plurality of genomic loci of each respective oncogenic pathogen in the plurality of oncogenic pathogens. [Paragraphs 408-410 of Lo et al. teach hybridization of the nucleic acids. Paragraph 276 of Lo et al. teaches analysis of loci during hybridization assays.]
The method comprises obtaining a plurality of sequence reads of the nucleic acid hybridized to the probe set. [Claim 1 of Lo et al. teaches obtaining sequence reads from a subject.]
The method comprises determining, for each respective sequence read in the plurality of sequence reads, whether the respective sequence read aligns to a human reference genome through an alignment of the respective sequence read. [Claim 1 of Lo et al. teaches determining whether the sequence read is from the reference genome. Paragraph 205 of Lo et al. teaches mapping through aligning.]
The method comprises determining, for each respective sequence read in the plurality of sequence reads that fail to align to the human reference genome, whether the respective sequence read aligns to a reference genome of a first oncogenic pathogen in the plurality of oncogenic pathogens. [Claim 1 of Lo et al. teaches determining whether the sequence read is from the pathogen. Paragraph 205 of Lo et al. teaches mapping through aligning.]
The method comprises tracking, for each respective oncogenic pathogen in the plurality of oncogenic pathogens, a number of sequence reads in the plurality of sequence reads that both fail to align to the human reference genome and align to a reference genome of the respective oncogenic pathogen, thereby obtaining a sequence read count for each oncogenic pathogen in the plurality of oncogenic pathogens. [Figure 60 and paragraph 68 of Lo et al. teach a count-based determination of level of pathogenicity.]
The method comprises using the sequence read count for each oncogenic pathogen in the plurality of oncogenic pathogens to ascertain whether the subject is afflicted with an oncogenic pathogen. [Figure 61 and paragraph 69 of Lo et al. teach determination is a subject is afflicted with the pathogen.]
Claim 128 is drawn to similar subject matter as claim 1, except claims 128 is drawn to a non-transitory computer readable medium. [Figure 62 of Lo et al. illustrates the computer limitations.]
Claim 130 is drawn to similar subject matter as claim 1, except claims 128 is drawn to a computer system with a processor. [Figure 62 of Lo et al. illustrates the computer limitations.]
With regard to claims 2 and 5-6, claim 24 of Lo et al. lists oncogenic viruses that overlap with the listing in Table 1 and include species of the papillomavirus family.
With regard to claim 24, Figures 56 and 58 of Lo et al. illustrates the results from reads from at least 100 different loci.
With regard to claim 33, paragraphs 137 and 243 teach at least 25 million sequence reads with an average length of at least 50 nucleotides.
With regard to claim 49, paragraph 73 of Lo et al. teaches that the sample can comprise blood or saliva.
With regard to claims 60-61 and 65, claims 1 and 24 of Lo et al. output a report of whether the subject is afflicted with a pathogen, and, if so, the cancer and pathogen type in the subject. Paragraph 273 of Lo et al. reports treatment modalities for cancer.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
Claim(s) 1-3, 5-7, 24, 33, 49, 56, 60-61, 65-66, 128, and 130 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lo et al. in view of The Cancer Genome Atlas Network “TCGAN” [Nature, volume 517, 2015, pages 576-582].
Claims 3 and 7 are further limiting comprising mapping against a reference genome of the oncogenic virus to determine the strain of the oncogenic virus.
Claim 56 is further limiting comprising requiring the respective set of nucleic acid probes for the corresponding plurality of genomic loci of each respective oncogenic pathogen to include probes collectively representing at least four of the portions listed in Table 2.
Claim 66 teaches antiviral treatments for HPV+ cancer and chemotherapy or immunotherapy for HPV-cancer.
Lo et al. teaches using sequencing alignment and counts to determine if a subject is infected with an oncogenic pathogen. Paragraph 273 of Lo et al. teaches general treatment modalities of cancer. Claim 24 of Lo et al. teaches HPV as a type of oncogenic pathogen.
Lo et al. does not teach complete mapping of genomic characterizations or specific antiviral therapy for HPV+ cancer.
The document of TCGAN studies comprehensive genomic characterization of head and neck squamous cell carcinomas [title]. The abstract of TCGAN teaches a complete genomic profiling of 279 head and neck squamous cell carcinomas. Pages 576-577 of TCGAN teach antivirals to treat HPV+ cancer.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the cancer diagnostic technique of Lo et al. by use of the comprehensive mapping technique of TCGAN wherein the motivation would have been that TCGAN gives a more comprehensive set of data to analyze cancer [abstract of TCGAN]. While TCGAN does not list the specific genomic portions in Table 2 of the specification, it would have been obvious to try the genetic portions in Table 2 of the specification because the analysis and diagnostic techniques of Lo et al. and TCGAN are robust and generally applicable, independent of the identity of the input gene.
Double Patenting
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.
Double Patenting Rejection #1:
Claims [69, 70, or 66] rejected on the ground of nonstatutory double patenting as being unpatentable over claims [1 or 13] of U.S. Patent No. 11,043,304 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn using training and classification to differentiate between HPV+ and HPV- cancer, particularly in cervical cancer.
While the claims of ‘304 do not list the genes in Table 21 of the specification, it would have been obvious to try the genes in Table 21 of the specification because the analysis and diagnostic techniques of the claims of ‘304 are robust and generally applicable, independent of the identity of the input gene.
Double Patenting Rejection #2:
Claims [69, 71, or 66] rejected on the ground of nonstatutory double patenting as being unpatentable over claims [1 or 13] of U.S. Patent No. 11,043,304 B2 in view of TCGAN. Although the claims at issue are not identical, they are not patentably distinct from each other because both sets of claims are analogously drawn using training and classification to differentiate between HPV+ and HPV- cancer. However, the claims of ‘304 are particular to cervical cancer and not head and neck squamous carcinomas.
The document of TCGAN studies comprehensive genomic characterization of head and neck squamous cell carcinomas [title]. The abstract of TCGAN teaches a complete genomic profiling of 279 head and neck squamous cell carcinomas. Pages 576-577 of TCGAN teach antivirals to treat HPV+ cancer.
It would have been obvious to someone of ordinary skill in the art at the time of the effective filing date of the instant application to modify the cancer classification technique of the claims of ‘304 by use of the head and neck squamous carcinoma of TCGAN because it is obvious to substitute known elements in the prior art to yield a predictable result. The head and neck squamous cell carcinomas of TCGAN are an alternative to the cervical cancer of the claims of ‘304. While the claims of ‘304 and TCGAN do not list the genes in Table 21 of the specification, it would have been obvious to try the genes in Table 21 of the specification because the analysis and diagnostic techniques of the claims of ‘304 and TCGAN are robust and generally applicable, independent of the identity of the input gene and the type of cancer.
Allowable Subject Matter
Claims 42 and 69-71 are free of the prior art. The prior art does not teach the hash table and seeding algorithm recited in claim 42. The prior art does not teach the application of machine learning to differentiate between HPV+ and HPV- cancer particular to cervical cancer and head and neck cancer recited in claims 69-71.
Related Prior Art
The Cancer Genome Atlas Research Network [Nature, volume 543, 2017, page 378] teaches an integrated genomic and molecular characterization of cervical cancer [title]. In this study, The Cancer Genome Atlas Research Network does a deep analysis into molecular characterization of 228 primary cervical cancers [abstract].
The document of Flygare et al. [US PGPUB 2018/0365375 A1; on IDS] study methods and systems for multiple taxonomic classification [title]. Rather than determining whether a read is associated with an oncogenic pathogen, the claims of Flygare et al. teach whether the sequence reads are associated with certain taxa.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/Primary Examiner, Art Unit 1686 14 August 2026
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