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 .
Status of Claims
Claims 1-20 are pending.
This communication is in response to the communication filed August 12, 2024.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
Use of the word “means” (or “step for”) in a claim with functional language creates a rebuttable presumption that the claim element is to be treated in accordance with 35 U.S.C. 112(f) (pre-AIA 35 U.S.C. 112, sixth paragraph). The presumption that 35 U.S.C. 112(f) (pre-AIA 35 U.S.C. 112, sixth paragraph) is invoked is rebutted when the function is recited with sufficient structure, material, or acts within the claim itself to entirely perform the recited function.
Absence of the word “means” (or “step for”) in a claim creates a rebuttable presumption that the claim element is not to be treated in accordance with 35 U.S.C. 112(f) (pre-AIA 35 U.S.C. 112, sixth paragraph). The presumption that 35 U.S.C. 112(f) (pre-AIA 35 U.S.C. 112, sixth paragraph) is not invoked is rebutted when the claim element recites function but fails to recite sufficiently definite structure, material or acts to perform that function.
Claim elements in this application that use the word “means” (or “step for”) are presumed to invoke 35 U.S.C. 112(f) except as otherwise indicated in an Office action. Similarly, claim elements that do not use the word “means” (or “step for”) are presumed not to invoke 35 U.S.C. 112(f) except as otherwise indicated in an Office action.
Claim limitations “input module”, “comparison module”, “output module”, and “amplification module” have been interpreted under 35 U.S.C. 112(f), because they use generic placeholders “module” coupled with functional language without reciting sufficient structure to achieve the function. Furthermore, the generic placeholder is not preceded by a structural modifier.
Since the claim limitation(s) invokes 35 U.S.C. 112(f), claims 11-20 have been interpreted to cover the corresponding structure described in the specification that achieves the claimed function, and equivalents thereof.
A review of the specification shows that the following appears to be the corresponding structure described in the specification for the 35 U.S.C. 112(f) limitations: Any module, unit, component, server, computer, computing device, mechanism, terminal or other device exemplified herein that executes instructions may include or otherwise have access to computer readable media such as storage media, computer storage media, or data storage devices (removable and/or non-removable) such as, for example, magnetic disks, optical disks, or tape. Computer storage media may include volatile and non-volatile, removable and non-removable media implemented in any method or technology for storage of information, such as computer readable instructions, data structures, program modules, or other data. Examples of computer storage media include RAM, ROM, EEPROM, flash memory or other memory technology, CD-ROM, digital versatile disks (DVD) or other optical storage, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage devices, or any other medium which can be used to store the desired information and which can be accessed by an application, module, or both. Any such computer storage media may be part of the device or accessible or connectable thereto. Any application or module herein described may be implemented using computer readable/executable instructions that may be stored or otherwise held by such computer readable media and executed by the one or more processors. (par. 84).
If applicant wishes to provide further explanation or dispute the examiner’s interpretation of the corresponding structure, applicant must identify the corresponding structure with reference to the specification by page and line number, and to the drawing, if any, by reference characters in response to this Office action.
If applicant does not intend to have the claim limitation(s) treated under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112 , sixth paragraph, applicant may amend the claim(s) so that it/they will clearly not invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, or present a sufficient showing that the claim recites/recite sufficient structure, material, or acts for performing the claimed function to preclude application of 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
For more information, see MPEP § 2173 et seq. and Supplementary Examination Guidelines for Determining Compliance With 35 U.S.C. 112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162, 7167 (Feb. 9, 2011).
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite systems and methods for cancer-cell specific transcription identification, which are statutory categories of inventions.
Specifically, the claims recite receiving nucleic acid data from one or more samples; determining variant allele fraction (VAF) of markers in ribonucleic acid (RNA) in the nucleic acid data and markers for deoxyribonucleic acid (DNA) in the nucleic acid data; comparing the VAF of the RNA relative to the DNA for each of the markers; and outputting the comparison as a quantification of cancer-cell specific changes in transcriptional output as a marker of prognosis or therapeutic response in cancer.
The dependent claims recite the limitations of independent claims and further describe limitations directed to comparing data, outputting no elevation and elevation indications, measuring cancer cells total RNA, outputting the relative fold amplification, markers being LOH-SNPs, samples from human tumors, determining expressed mutation burden, determining an adjusted genomic tumor mutation burden, and using quantification of cancer-cell specific changes.
The claim limitations are interpreted as being grouped within the “mental processes” grouping of abstract ideas because in this case, the claims involve a series of steps for collecting data, analyzing it, and outputting the results of the collection and analysis. See MPEP 2106.04. The claims are interpreted to recite concepts relating to tracking or organizing information. Accordingly, the claims recite an abstract idea.
This judicial exception is not integrated into a practical application. Integration into a practical application requires an additional element or a combination of additional elements in the claim to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the exception. Here, the additional elements of the claims use computer, processors, data storage, and various modules.
The claims merely use the additional elements as tools to perform abstract ideas and generally link the use of a judicial exception to a particular technological environment. The use of the additional elements as tools to implement the abstract idea and generally to link the use of the abstract idea to a particular technological environment does not render the claim patent eligible, because it requires no more than a computer performing functions that correspond to acts required to carry out the abstract idea. Specifically, the computer, processors, data storage, and various modules perform the steps or functions of receiving nucleic acid data, determining markers, comparing and analyzing data, and outputting the results.
Specification p. 84 states that any module, unit, component, server, computer, computing device, mechanism, terminal or other device exemplified herein that executes instructions may include or otherwise have access to computer readable media such as storage media, computer storage media, or data storage devices. Computer storage media may include volatile and non-volatile, removable and non-removable media implemented in any method or technology for storage of information, such as computer readable instructions, data structures, program modules, or other data. Examples of computer storage media include RAM, ROM, EEPROM, flash memory or other memory technology, CD-ROM, digital versatile disks (DVD) or other optical storage, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage devices, or any other medium which can be used to store the desired information and which can be accessed by an application, module, or both. Any such computer storage media may be part of the device or accessible or connectable thereto. Any application or module herein described may be implemented using computer readable/executable instructions that may be stored or otherwise held by such computer readable media and executed by the one or more processors. Thus, the additional elements are interpreted as extra solution activity and are generally linking the abstract idea to a technical environment.
The additional elements do not show an improvement to the functioning of a computer or to any other technology, rather the additional elements perform general computing functions and do not indicate how the particular combination improves any technology or provides a technical solution to a technical problem. See Apple v. Ameranth, 842 F.3d 1229, 1240 (Fed. Cir. 2016). The additional elements do not use the exception to affect a particular treatment or prophylaxis for a disease, do not apply the exception using particular machines, and do not effect a transformation or reduction of a particular article to a different state or thing, rather the computer elements are generally stated as to their structure and function and are only used to identify markers of cancer instead of directly providing specific treatment or prophylaxis. Therefore, the additional elements do not impose any meaningful limits on practicing the abstract idea and the additional limitations are not indicative of materializing into a practical application. Accordingly, the claim is directed to an abstract idea.
Generic computer elements recited as performing generic computer functions that are well-understood, routine, or conventional activities amount to no more than implementing the abstract idea with a computerized system (Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network); buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network and performing repetitive calculations); Bancorp Services v. Sun Life, 687 F.3d 1266, 1278, 103 USPQ2d 1425, 1433 (Fed. Cir. 2012) ("The computer required by some of Bancorp’s claims is employed only for its most basic function, the performance of repetitive calculations, and as such does not impose meaningful limits on the scope of those claims."); See MPEP 2106.05(d) and July 2015 Update: Section IV). Here, the claim limitations are similar to sending and receiving the nucleic acid data, and performing repeated calculations of the VAF comparisons for each of the RNA and DNA markers.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because, as discussed above with respect to integration of the abstract idea into a practical application, the use of additional elements to perform the steps of the claims amount to no more than using computer related devices to automate or implement the abstract idea of cancer-cell specific transcription identification.
The use of a computer or processor to merely automate or implement the abstract idea cannot provide significantly more than the abstract idea itself. (See MPEP 2106.05(f) where mere instructions to apply an exception does not render an abstract idea patent eligible). There is no indication that the additional limitations alone or in combination improves the functioning of a computer or any other technology, improves another technology or technical field, or effects a transformation or reduction of a particular article to a different state or thing. Therefore, the claims are not patent eligible.
In conclusion, the claims are directed to the abstract idea of cancer-cell specific transcription identification. The claims do not provide an inventive concept, because the claims do not recite additional elements or a combination of elements that amount to significantly more than the judicial exception of the claims. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology, and the collective functions merely provide conventional computer implementation. Therefore, whether taken individually or as an order combination, the claims are nonetheless rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
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.
Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12,080,381. Although the claims at issue are not identical, they are not patentably distinct from each other because the pending claims recite the limitations of the patented claims. Pending claims 1-10 recite similar limitations as pending claims 11-20. Pending claims 5 and 15 are rejected for being dependent on rejected claims.
Pending claim 1 recites
Patented claim 1 recites
A computer-implemented method for cancer-cell specific transcription identification, the method comprising: receiving nucleic acid data from one or more samples;
A computer-implemented machine learning method for identifying cancer-cell specific transcriptional output for provision of immunotherapy treatment, the method comprising:
determining variant allele fraction (VAF) of markers in ribonucleic acid (RNA) in the nucleic acid data and markers for deoxyribonucleic acid (DNA) in the nucleic acid data;
determining, by the processor, variant allele fraction (VAF) of markers in ribonucleic acid (RNA) in the nucleic acid data and markers for deoxyribonucleic acid (DNA) in the nucleic acid data;
comparing the VAF of the RNA relative to the DNA for each of the markers; and
comparing, by the processor, the VAF of the RNA relative to the DNA for each of the markers;
outputting the comparison as a quantification of cancer-cell specific changes in transcriptional output as a marker of prognosis or therapeutic response in cancer.
quantifying, by the processor, cancer-cell specific changes in transcriptional output for each of the markers using the comparison of the VAF of the RNA relative to the DNA…outputting, by the processor, the response to immunotherapy treatment for provision of the immunotherapy treatment of cancer.
Pending claim 2 recites: wherein comparing the VAF of the RNA relative to the DNA for each of the markers comprises determining a VAF difference, a VAF ratio, and an allelic ratio.
Patented claim 2 recites: wherein comparing the VAF of the RNA relative to the DNA for each of the markers comprises determining a VAF difference, a VAF ratio, and an allelic ratio.
Pending claim 3 recites: wherein the quantification of cancer-cell specific changes in transcriptional output comprises outputting no elevation in cancer global transcription when the VAF indicates that the markers in the RNA and the DNA are similar, and outputting elevation in cancer global transcription when the VAF indicates that the markers in the RNA are elevated relative to the markers in the DNA.
Patented claim 3 recites: wherein the quantification of cancer-cell specific changes in transcriptional output comprises no elevation in cancer global transcription when the VAF indicates that the markers in the RNA and the DNA are similar, and elevation in cancer global transcription when the VAF indicates that the markers in the RNA are elevated relative to the markers in the DNA.
Pending claim 4 recites: wherein the samples comprise both cancer cells and normal cells, and wherein determining the VAF in the RNA comprises measuring the cancer cells total RNA output and measuring the normal cells total RNA output.
Patented claim 4 recites: wherein the samples comprise both cancer cells and normal cells, and wherein determining the VAF in the RNA comprises measuring the cancer cells total RNA output and measuring the normal cells total RNA output.
Pending claim 6 recites: wherein the markers comprise somatic single nucleotide substitutions and single nucleotide polymorphisms in regions of loss-of-heterozygosity (LOH-SNPs).
Patented claim 5 recites: wherein the markers comprise somatic single nucleotide substitutions and single nucleotide polymorphisms in regions of loss-of-heterozygosity (LOH-SNPs).
Pending claim 7 recites: wherein the one or more samples come from human tumors whose RNA was derived from bulk tissue.
Patented claim 6 recites: wherein the one or more samples come from human tumors whose RNA was derived from bulk tissue.
Pending claim 8 recites: determining expressed mutation burden due to the quantification of cancer-cell specific changes in transcriptional output for identification of patients that would respond to immune checkpoint inhibitor (ICI) therapy.
Patented claim 7 recites: wherein the mutation burden comprises expressed mutation burden and the immunotherapy comprises immune checkpoint inhibitor (ICI) therapy.
Pending claim 9 recites: further comprising determining an adjusted genomic tumor mutation burden (TMB) value based on the expressed TMB using a linear regression model with the expressed TMB as a predictor variable and genomic TMB as an outcome variable.
Patented claim 8 recites: wherein determining the mutation burden further comprises determining an adjusted genomic tumor mutation burden (TMB) value based on the expressed TMB using a linear regression model with the expressed TMB as a predictor variable and genomic TMB as an outcome variable.
Pending claim 10 recites: further comprising using the quantification of cancer-cell specific changes in transcriptional output to identify patients with non-hypermutant tumors that would respond to immunotherapy.
Patented claim 9 recites: wherein determining the mutation burden comprises determining non-hypermutant tumors that would respond to immunotherapy.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY M. PATEL whose telephone number is (571)272-6793 and email is jay.patel2@uspto.gov. The examiner can normally be reached on Monday-Friday 8AM-4:30PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Peter H. Choi can be reached on (469)295-9171. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JAY M. PATEL/Primary Examiner, Art Unit 3686
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