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 .
Information Disclosure Statement
The IDS filed 2/14/2025 and 1/12/2022 have been considered by the Examiner.
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 62/988306 filed 3/11/2020 is acknowledged.
Claim Election/Restriction
Election with Traverse
Applicant's election with traverse of claim 22 and claim 35 in the reply filed on 2/14/2025 is acknowledged. The traversal is on the ground(s) that the species are not mutually exclusive. This is found persuasive and the restriction is withdrawn.
Status of Claims
Amendments to the claims are acknowledged. Claims 57-62 are new.
Claims 1, 8-30, 35, 37, and 39 are under examination.
Claims 2-7, 31-34, 36, 38 and 40-56 are cancelled.
Claim Rejections - 35 USC § 101
The instant rejection is maintained from the previous Office Action filed 6/12/2025 and modified in view of Amendments filed 12/12/2025. Suggestions for amendments follows the Response to Arguments.
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, 8-30, 35, 37, 39 and 57-62 are 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
1, 8-30, 35, 37, 39 and 57-62 are drawn to a method, so a process.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s):
1. generating or providing, by the computer, at least one tumor variant dataset comprising a plurality of reference tumor-related genetic variants.
This step reads on a process of observing reference sample data and generating a tumor variant dataset. The process can be performed by the human mind and is therefore an abstract idea.
2. wherein the tumor variant dataset comprises frequency of observance data among reference samples that comprises reference bodily fluid samples and/or reference non-bodily fluid samples for one or more tumor-related genetic variants in the population of reference tumor-related genetic variants, and wherein the reference samples are obtained from a single reference subject and/or from different reference subjects having an identical cancer type.
This limitation describes the data from which the tumor variant dataset is generated and describes how the data was generated and where the samples were taken. The limitation further limits the abstract idea. The limitation also recites a natural correlation between tumor related genetic variants and cancer.
2. determining, by the computer, one or more ratios of the frequency of observance data between the reference samples for at least one tumor-related genetic variants in the plurality of reference tumor-related genetic variants to produce at least one MAF variance and/or relative prevalence dataset.
This step recites a mathematical relationship which is ratios of frequency between samples and generic variants and performing math. The mathematical relationships and doing math is an abstract idea.
3. generating, by the computer, at least one set of probabilities of non-tumor origin from the MAF variance and/or relative prevalence dataset.
This step reads on math and a mental process which is generating a probability and is therefore an abstract idea.
4. identifying, using the set of probabilities of non-tumor origin, nucleic acid variants detected in the cfNA sample obtained from the test subject are non-tumor origin nucleic acid or are tumor origin nucleic acid variants. .
This step reads on a process that can be performed by the human mind by analyzing probabilities to determine tumor origin or non-tumor origin nucleic acids. The step is therefore an abstract idea.
Dependent claims 1, 8-24, 26, 28-30, 35, 37, 39 and 57-62 are drawn to describing how the data was gathered and further steps that can be performed by the human mind or with math, and are therefore also judicial exceptions. Claims 14-15 recite a machine learning model which reads on mathematics performed on a computer. Claims 57-62 list different tumor origin variant genes which describe the information being analyzed and identified by the abstract idea.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a step of identifying, using probabilities of non-tumor origin, variants in a cfNA sample as being tumor origin nucleic acid or non-tumor origin nucleic acid variants. Claim 1 further results in “causing” to administer one or more therapies based on the tumor origin nucleic acid variants. Claim 1 does not integrate the judicial exception into the step of treating because it does not recite how the determined probabilities are used to identify a tumor origin variant that would result in a treatment. The claims merely recites “using probabilities” and administering “based on the tumor origin nucleic acid variants.” The treatment step is tangential and a just “apply it” limitation as described in MPEP 2106.05(f).
Additionally, claim 1 does not recite a particular treatment as required in order to be a “practical application.”
Also, the administration step of claim 1 is a conditional limitation based on identifying tumor origin nucleic acid variants. In the case of identification of non-tumor origin nucleic acids, the step of administering is not performed. See MPEP 2111.04 “Contingent Limitations” stating that the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.
New claims 57-62 recite specific tumor origin variant genes and specific treatments. However, claim 1 recites a conditional limitation of identifying non-tumor origin nucleic acid or tumor origin nucleic acid variants. In the case of identification of non-tumor origin nucleic acids, the steps of administering are not performed. See MPEP 2111.04 “Contingent Limitations.”
Claim 27 also recites a step of administering therapies to the test subject however, claim 27 is also conditional and relies on identification of “tumor origin” nucleic acids. Additionally the recited selected therapies are not “particular treatments.”
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:
1. obtaining cfNA sample from the test subject, as in claim 25.
2. administering therapies to the test subject to treat a cancer type when one or more tumor origin nucleic variants are detected, as in claims 1, 27 and 57-62.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because obtaining cell free nucleic acid samples is well known, routine and conventional. The step is also an extra solution activity of data gathering, as described in MPEP 2106.05(g). The steps of administering known cancer treatments including those recited in claims 57-62 is well known, routine and conventional.
Other elements of the method include “partially using a computer” recited in the preamble, 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.
Response to Arguments
Applicant's arguments filed 12/12/2025 have been fully considered but they are not persuasive.
Applicants argue (Remarks, page 9-10) that the instant claims are directed to the use of different treatment regimens given identified genes or genetic status. Applicants cite the decision in Vanda. Applicants argue that particularized treatment cause administration of a therapy based on the identified tumor origin nucleic acid variants. Applicants argue (Remarks, page 10, par. 2) that claim 1 does not contain contingent language because the recited identification step will always be performed.
In response, claim 1 indeed recites a definitive identification step of “identifying,” nucleic acid variants in a sample are non-tumor origin nucleic acids or are tumor origin nucleic acids. However, the claim goes on to recite “and causing to administer one or more therapies to the test subject selected based on the tumor origin nucleic acid variants.” The claim encompasses a process where non-tumor origin nucleic acids are identified (and tumor origin nucleic acids are not identified) and therefore the therapy administration would not be performed because it is based on the tumor origin nucleic acid. The same embodiment applies to claims 57-62 which rely on the identification of specific tumor origin nucleic acid variants.
Furthermore, claim 1 does not recite a particular treatment and therefore does not meet the standard for a practical application under Step 2 Prong Two.
Additionally, as set forth above, claim 1 does not integrate the judicial exception into the step of treating because it does not recite how the determined probabilities are used to identify a tumor origin nucleic acid variant that would result in a treatment. The claim merely recites “using probabilities” and administering “based on the tumor origin nucleic acid variants.” The treatment step is a just “apply it” limitation as described in MPEP 2106.05(f).
Suggestion for Amendments:
It is suggested that (1) claim 1 be amended to recite a definitive step of identifying a tumor origin nucleic acid and (2) the specific genes and therapies of claims 57-62 be incorporated into claim 1 because these claims do include specific treatments. (3) alternatively, a particular class of treatments (e.g. immunotherapy) encompassing the treatments of claims 57-67 may be recited in claim 1. (4) the step of generating and using probabilities should be integrated with the step of identifying a tumor origin nucleic acid variant by reciting how the probabilities are used.
Claim Rejections - 35 USC § 112-2nd paragraph
The rejection of claims 1, 8-30, 35, 37, and 39 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of Applicant’s amendments filed 12/12/2025. The instant rejection is necessitated by Applicant’s amendment filed 12/12/2025.
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 1, 8-30, 35, 37, 39 and 57-62 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 pre-AIA the applicant regards as the invention.
Claim 1 has been amended to recite “causing to administer one or more therapies” based on tumor origin nucleic acid variants. It is not clear what steps are performed to initiate the recited “causing.” The identification step includes identifying non-tumor origin nucleic acids or tumor origin nucleic acids. Therefore it is not clear what causes the administration of the therapies. It is suggested that the claim instead recite a definitive step of identifying tumor origin variants and simply recite “administering” a particular therapy based on the tumor origin variants.
Claim 37 recites “the selected one or more therapies.” There is lack of antecedent basis support for this limitation. Claim 1 from which claim 37 depends does not include a step of selecting or recite selected therapies. It is suggested that the word “selected” be deleted.
Claim 58 recites that the tumor origin variants “support” a determination of TMB-High status. The metes and bounds of “support” are not clear. It is not clear if “support” is intended to mean “indicates” or if “support” means “is used for.” It is suggested that “support” be replaced with “indicates.”
Claim Rejections - 35 USC § 103
The rejection of claims 1, 8-30, 35, 37, and 39 under 35 U.S.C. 103(a) as being unpatentable over Jaimovich et al. (US 2019/0385700) is withdrawn in view of Applicant’s amendments and arguments filed 12/12/2025.
E-mail communication 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
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anna Skibinsky whose telephone number is (571) 272-4373. The examiner can normally be reached on 12 pm - 8:30 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Ram Shukla can be reached on (571) 272-7035. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Anna Skibinsky/
Primary Examiner, AU 1635