DETAILED ACTION
Applicant's response, filed 08/10/2026, has been fully considered.
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 .
Priority
This application filed 08/09/2022 is a Continuation of 15793830 , filed 10/25/2017, now U.S. Patent # 11459616, which is a Continuation of PCT/US17/58099, filed 10/24/2017, and claims priority from Provisional Application 62507154, filed 05/16/2017, from Provisional Application 62450541, filed 01/25/2017, and from Provisional Application 62411929, filed 10/24/2016. The claims are therefore examined as filed on 10/24/2016, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Election/Restrictions
Claims 17, 19, and 30 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 08/10/2026.
Applicant’s election without traverse of claims 16, 18, and 29 in the reply filed on 08/10/2026 is acknowledged.
Claim Status
Claims 1-30 are pending.
Claims 17, 19, and 30 are withdrawn.
Claims 1-16, 18, and 20-29 are directed to the elected invention.
Claims 1-16, 18, and 20-29 are examined.
Claims 1-16, 18, and 20-29 are rejected.
Information Disclosure Statement
The Information Disclosure Statements are in compliance with the provisions of 37 CFR 1.97. Accordingly, all references have been considered.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-16, 18, and 20-29 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-16, 18, and 20-29 are directed to a process (a method of determining a level of cancer in a subject).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. The claims recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Determining, based on sequence reads from a second biological sample of the subject, an amount of nucleic acid molecules in the second biological sample that are from a pathogen and have a size within a given range (mental process/mathematical concept; the human mind is capable of determining an amount of nucleic acid molecules from sequencing reads, and determining an amount or numerical value from data is equivalent to performing a calculation; claim 1)
Normalizing an amount of nucleic acid molecules from the second biological sample that are from the pathogen and have a size within the given range (mental process/mathematical concept; the human mind is capable of normalizing data, and normalizing data is equivalent to performing a calculation; claim 4)
Determining a size ratio of a first proportion of sequence reads of nucleic acid molecules from the second biological sample that align to a reference genome of the pathogen with a size within the given range; and a second proportion of sequence reads of nucleic acid molecules from the second biological sample that align to a human reference genome with a size within the given range (mental process/mathematical concept; the human mind is capable of determining a ratio from data, and doing so is a mathematical concept; claim 6)
Comparing a size ratio to a cutoff (mental process; the human mind is capable of comparing a numerical value to a cutoff value; claim 8)
Determining a size index, wherein the size index is an inverse of the size ratio (mental process/mathematical concept; the human mind is capable of taking the inverse of a value to determine a size index, and doing so is equivalent to performing a calculation; claim 10)
Comparing the size index to a second cutoff value (mental process; the human mind is capable of comparing a numerical value to a cutoff value; claim 11)
Dependent claims 2-3, 7, 9, 12, 13, and 21 further limit the abstract ideas recited in the independent claims, and do not change their characterization as abstract ideas.
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claim 1 recites the limitation of determining a first amount of cell-free nucleic acid molecules from a pathogen in a first biological sample from the subject. Claim 5 and 28 further recites the additional element of massively parallel sequencing of the nucleic acid molecules to generate sequence reads, claim 14 recites assays for determining the amounts with claims 15-20 further describing aspects of the assays, claims 25-27 and 29 describe the sample, and claims 22-24 recite the additional element of amplification/PCR/qPCR.
While the claims recite the additional element of gathering data from samples in the form of sequencing/assays/PCR, such steps that only amount to necessary data gathering for ana analysis , without any technical details of how the data is obtained/output that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). Non-particular instructions to gather or produce data via PCR or assays do not provide an inventive concept, and are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Determining the level of a biomarker in blood by any means” from Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017), “Using polymerase chain reaction to amplify and detect DNA, from Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015), and “Analyzing DNA to provide sequence information or detect allelic variants”, from Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546 are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Claims Without an Art Rejection
No art rejection is applied to claims 1-16, 18, and 20-29. Close art, for example YIP 2014 (cited on the 892 form), and Chan 2003 (cited on the IDS filed 9/25/2018), while teaching methods of detecting amounts of cell-free nucleic acid from the Epstein-Barr virus in patient samples to determine a level of nasopharyngeal cancer, does not teach the instant combination of determining a first amount of cell-free nucleic acid molecules from a pathogen in a first biological sample from the subject, a second amount of nucleic acid molecules in a second biological sample that are from the pathogen and have a size within a given range, and determining a level of cancer of the subject based on the first amount and the second amount. No combinable art before the effective filing date could be found to render the claims as obvious.
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.
Rejection over Patent No. 11459616
Claims 1-16, 18, and 20-29 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5, 7-10, 12-18, 20, and 22-31 of U.S. Patent No. 11459616. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the patent anticipate the claims of the present application.
Claim 1 of the present application is anticipated by claim 1 combined with claim 6 of Patent No. 11459616: claim 1 of the patent contains all of the limitations of the present claim 1 except for defining the pathogen as a virus, and claim 6 of the patent defines the pathogen as a virus.
Claim 2 of the present application is identical to claim 2 of the patent.
Claim 3 of the present application is identical to claim 3 of the patent.
Claim 4 of the present application is identical to claim 4 of the patent.
Claim 5 of the present application is identical to claim 5 of the patent.
Claim 6 of the present application is identical to claim 7 of the patent.
Claim 7 of the present application is identical to claim 8 of the patent.
Claim 8 of the present application is identical to claim 9 of the patent.
Claim 9 of the present application is identical to claim 10 of the patent.
Claim 10 of the present application is identical to claim 12 of the patent.
Claim 11 of the present application is identical to claim 13 of the patent.
Claim 12 of the present application is identical to claim 14 of the patent.
Claim 13 of the present application is identical to claim 15 of the patent.
Claim 14 of the present application is identical to claim 16 of the patent.
Claim 15 of the present application is identical to claim 17 of the patent.
Claim 16 of the present application is identical to claim 18 of the patent.
Claim 18 of the present application is identical to claim 20 of the patent.
Claim 20 of the present application is identical to claim 22 of the patent.
Claim 21 of the present application is identical to claim 23 of the patent.
Claim 22 of the present application is identical to claim 24 of the patent.
Claim 23 of the present application is identical to claim 25 of the patent.
Claim 24 of the present application is identical to claim 26 of the patent.
Claim 25 of the present application is identical to claim 27 of the patent.
Claim 26 of the present application is identical to claim 28 of the patent.
Claim 27 of the present application is identical to claim 29 of the patent.
Claim 28 of the present application is identical to claim 30 of the patent.
Claim 29 of the present application is identical to claim 31 of the patent.
Rejection over Patent No. 10633713
Claims 1-4, 6-7, 10, 13, 16, 22-23 and 27 are rejected on the ground of nonstatutory double patenting as being unpatentable over at least claims 4-7, 10, 15-16, 25, 39, and 44 of U.S. Patent No. 10633713. Although the claims at issue are not identical, they are not patentably distinct from each other because the combined claims of the patent anticipate the claims of the present application.
Claim 1 of the present application is anticipated by claims 39 in view of claim 16; claim 39 contains all of the limitations of the present claim 1 except for specifying that the pathology determined in cancer, and claim 16 recites that the level of pathology is a level of cancer.
Claim 2 of the present application is anticipated by claim 5 of the patent combined with the above claims.
Claim 3 of the present application is anticipated by claim 4 of the patent combined with the above claims.
Claim 4 of the present application is anticipated by claim 44 of the patent combined with the above claims.
Claim 6 of the present application is anticipated by claim 5 of the patent combined with the above claims.
Claim 7 of the present application is anticipated by claim 6 of the patent combined with the above claims.
Claim 10 of the present application is anticipated by claim 7 of the patent combined with the above claims.
Claim 13 of the present application is anticipated by claim 25 of the patent combined with the above claims.
Claim 16 of the present application is anticipated by claim 15 of the patent combined with the above claims.
Claim 22 and 23 of the present application are anticipated by claim 10 of the patent combined with the above claims.
Claim 27 of the present application are anticipated by claim 39 of the patent combined with the above claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
YIP 2014 “Application of circulating plasma/serum EBV DNA in the clinical management of nasopharyngeal carcinoma” reviews methods of detecting amounts of cell-free nucleic acid from the Epstein-Barr virus in patient samples to determine a level of nasopharyngeal cancer
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R. Skowronek can be reached at (571) 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARY C LEVERETT/Examiner, Art Unit 1687
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