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 .
Application Status
This action is written in response to applicant’s correspondence received on 6/30/2025. Claims 1-3, 5-9, 13, 17-26, and 29 are pending. Claims 1, 3, 5-9, and 19-25 have been amended. Claims 4, 10-12, 14-16, 27-28, and 30-32 have been cancelled. All pending claims are currently under examination.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow. This Office Action is Final.
Claim Rejections - 35 USC § 101 – Updated in Response to Amendment
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 1-3, 5-9, 13, 17-26, and 29 are rejected under 35 U.S.C. 101 because the claimed invention is directed to naturally occurring phenomenon without significantly more.
Regarding claim 1, claim 1 recites a method of assessing a sample from a transplant subject, the method comprising a) obtaining cell-free DNA from the sample, b) determining the product of an amount of donor-specific cell-free DNA (DS-cfDNA) and an amount of total cf-DNA in the sample; and b) performing an assay on the sample to measure an amount of donor-specific cell-free DNA (DS cf-DNA) and an amount of total cf-DNA in the sample c) determining a product of the amount of DS cf- DNA and the amount of total cf-DNA in the sample; and d) reporting and/or recording the product. Thus, claim 1 recites steps of data manipulation and analysis, where such steps are judicial exceptions because they recite an abstract concept (i.e., a mathematical relationship). With regards to Step 1 of the Subject Matter Eligibility Test (MPEP 2106), claim 1 recites a process. Regarding Step 2A, prong I, claim 1 recites the abstract concept of a mathematical relationship (MPEP 2106.04(a)(2)). Regarding Step 2A, prong II, claim 1 recites the additional element of “reporting and/or recording the product.” However, recitation of “reporting and/or recording the product” amounts to insignificant extra-solution activity, as these are mere instructions to apply a judicial exception (see MPEP 2106.05(f)). Claim 1 also recites the additional elements of obtaining cell-free DNA from the sample and performing an assay on the sample to determine the amount of donor-specific and cf-DNA and total cf-DNA in the sample. However, with regards to Step 2A, prong II, the action of determining the level of a biomarker in blood is mere data gathering and amounts to insignificant extra-solution activity per MPEP 2106.05(g). Furthermore, MPEP 2106.05(g) states that performing clinical tests to obtain input for an equation, as recited in claim 1, is also mere data gathering and amounts to insignificant extra-solution activity Thus, the additional elements recited in claim 1 do not integrate the subject matter into a practical application.
Regarding Step 2B, the additional elements recited in claim 1, “reporting and/or recording the product” does not amount to significantly more than the judicial exception because reporting or recording a value is simply well-understood, routine activity, and therefore does not transform the claim into patent eligible subject matter. Furthermore, the limitations of obtaining cell-free DNA from a sample and determining the amount of DS cf-DNA and total cf-DNA amounts to “determining the level of a biomarker in blood by any means,” which MPEP 2106.05(d) section II states is an example of well-understood, routine, conventional activity. Furthermore, detecting DNA in a sample is also offered as an example of well-understood, routine, conventional activity per MPEP 2106.05(d) section II. Thus, with regards to Step 2B, the additional elements recited in claim 1 do not amount to significantly more than the judicial exception recited, as the additional steps are well-understood, routine, and conventional per MPEP 2106.05(d). Claim 1 is therefore directed to a judicial exception without significantly more and is rejected under 35 USC 101.
Regarding claims 2-3, these claims recite the judicial exceptions of claim 1. Claim 2 further recites that additional products are calculated from a sample taken from the subject at different time points, and claim 3 recites that samples are taken monthly or bi-monthly. Claims 2-3 therefore recite the abstract mental process of performing a mathematical operation (Step 2A, prong I). Claims 2-3 recite the additional element that the products are calculated from sample derived from a subject at different timepoints. However, recitation of the limitation that the sample is taken over time does not integrate the judicial exception into a practical application because determining the level of a biomarker in blood is mere extra-solution activity (Step 2A, prong II, MPEP 2106.05(g)). Claims 2-3 furthermore do not recite limitations which transform the claim into significantly more because such a step as collecting a patient sample to measure a biomarker is simply a routine data gathering step that is well-understood and known in the art per MPEP 2106.05(d) (Step 2B). Claims 2-3 are therefore drawn to patent ineligible subject matter and is rejected under 35 USC 101.
Regarding claim 5, claim 5 recites the additional mental process of “comparing the product to one or more threshold values and/or one or more product values from one or more prior time points.” Thus, claim 5 recites the additional judicial exception of “comparing” data to a “threshold” (i.e., a mathematical value). Claim 5 recites abstract mental processes related to abstract mathematical concepts (Step 2A, prong I). Claim 5 does not recite additional elements (Steps 2A prong II and Step 2B). Claim 5 is therefore drawn to a judicial exception without significantly more and is rejected under 35 USC 101.
Regarding claim 6, claim 6 recites the additional judicial exception of “determining and/or assigning a risk to the subject based on a comparison of the products to one or more threshold values and/or one or more product values from one or more prior time points.” Thus, claim 6 is drawn to the abstract mental process of “determining/assigning” and “comparing,” (Step 2A, prong I). Claim 6 does not recite any additional elements (Step 2A, prong II, and Step 2B). Claim 6 is therefore rejected under 35 USC 101.
Regarding claim 7, claim 7 recites the judicial exceptions of “determining” and “comparing” values/products (i.e., mathematical calculations and relationships) and “determining a treatment or monitoring regimen for a subject.” These are judicial exceptions because they are drawn to mental processes (Step 2A, prong I). Claim 7 recites the additional elements of obtaining cell-free DNA in a sample from the transplant subject and performing an assay to determine the amount of DS cf-DNA and total cf-DNA. However, this limitation does not integrate the subject matter into a practical application nor transform the claim into significantly more than the recited judicial exception because the remaining elements of the claim amount to mere routine data-gathering steps which are merely extra-solution activity (i.e., determining a biomarker present in blood, performing clinical test to obtain input for an equation, Step 2A, prong II, MPEP 2106.05(g)) that is well-understood in the art (Step 2B, 2106.05(d) section II, which states that determining a biomarker in blood is routine by any means). Furthermore, recitation of “determining a treatment” lacks specificity and is overly general and therefore does not amount to significantly more than the judicial exception, and furthermore does not recite any actionable steps of a specific treatment (MPEP 2106). Claim 7 is therefore rejected under 35 USC 101.
Regarding claims 8 and 9, these claims simply recite obtaining a sample from a subject to measure a biomarker, with the judicial exceptions of determining a product (i.e., a mathematical relationship). These claims are therefore drawn to the judicial exceptions of claim 7 (Step 2A, prong I). Claims 8 and 9 recite the additional element of obtaining DNA from a subject at timepoints, which is simple extra-solution activity in the form of data gathering (Step 2A, prong II, see claim 7 rejection). Thus, claims 8 and 9 do not recite additional elements which integrate the judicial exceptions into a practical application. Claims 8-9 do not recite additional elements which transform the claims into significantly more than the judicial exceptions, as such data gathering to measure a biomarker in blood is routine, well-understood, and conventions per MPEP 2106.05(d) section II (Step 2B). Claims 8 and 9 are therefore rejected under 35 USC 101.
Regarding claim 13, claim 13 recites the judicial exceptions of claim 7 (Step 2A, prong I). Claim 13 recites the additional element of recording the values in a database or a report. However, recitation of this claim limitation amounts to mere extra-solution activity and does not integrate the judicial exception into a practical application or transform the claim into significantly more than the judicial exception (Steps 2A, prong II, Step 2B). Claim 13 is therefore rejected under 35 USC 101.
Regarding claims 17 and 18, these claims recite the judicial exceptions of relating a product value to another mathematical value (“thresholds”) as well as the relationship of such values. Claims 17 and 18 are therefore drawn to the judicial exception of abstract mathematical relationships and relating such relationships (a mental process) to risk characteristics (Step 2A, prong I). Claims 17 and 18 do not recite any additional elements (Steps 2A prong II and Step 2B). Claims 17 and 18 are therefore drawn to judicial exceptions without additional claim limitations and are rejected under 35 USC 101.
Regarding claim 19, claim 19 recites the judicial exception of “determining” a monitoring regimen based on the product of two values, or simply suggesting such monitoring. Claim 19 is therefore broadly drawn to the abstract mental process of “determining” (Step 2A, prong I). Claim 19 further recites determining the product of two values, which is an additional judicial exception because it relates to an abstract mental process/mathematical relationship (Step 2A, prong I). Claim 19 recites the additional element of suggesting monitoring in a subject; however, such claim language is recited broadly without specificity and therefore neither integrates the judicial exceptions into a practical application nor transforms the claim into significantly more than the judicial exceptions recited (Steps 2A prong II and Step 2B). Claim 19 is therefore rejected under 35 USC 101.
Regarding claims 20-21, these claims recite the judicial exceptions of claim 7 (Step 2A, prong I). Furthermore, these claims merely recite extra-solution activity in the form of routine data gathering (Steps 2A prong II and Step 2B). These claims therefore do not integrate the judicial exceptions into a practical application or transform the claim into patent eligible subject matter under 35 USC 101.
Regarding claim 22, claim 22 recites the judicial exceptions of claim 7 (Step 2A, prong I). Claim 22 is further most broadly interpreted to simply recite “suggesting” the use of an additional test. Recitation of “suggesting the use” of an additional test does not amount to a practical application of the judicial exceptions recited, as no actionable step is required by the claim (Steps 2A prong II). Furthermore, no specific “use” of an additional test is recited; the claim language is therefore lacking in specificity and does not transform the judicial exception into significantly more (Step 2B). Thus, claim 22 is simply drawn to the judicial exceptions of claim 1 and is not patentable subject matter under 35 USC 101.
Regarding claim 23, claim 23 recites the judicial exceptions of claim 7. Claim 23 is further most broadly interpreted to simply comprise “suggesting” a treatment. Recitation of “suggesting a treatment for the subject” does not amount to a practical application of the judicial exceptions because no actionable step is required by the claimed method (Step 2A, prong II). Furthermore, no specific “suggestion” of a treatment is recited; the claim language is therefore lacking in specificity and does not transform the judicial exception into significantly more (Step 2B). Thus, claim 23 is simply drawn to the judicial exceptions of claim 1 and is not patentable subject matter under 35 USC 101.
Regarding claims 24 and 25, these claims recite the judicial exceptions of claim 7 (Step 2A, prong I). Claim 24 recites the additional element of treating the subject in an attempt to integrate the judicial exception into a practical application. Claim 25 recites the additional element of providing information about a treatment to a subject. However, as outlined in MPEP section 2106.04(d)(2), these claim limitations are not sufficiently particular to a degree that would warrant the disclosed invention to be labeled as subject matter eligible. As currently written, claims 24 and 25 recite no specific and particular treatment and/or information provided to a subject which would transform the judicial exceptions into patent eligible subject matter, and therefore lack a practicable, actionable step. Recitation of “treating the subject” (claim 24) and “providing information about a treatment to the subject” (claim 25) is recited with a high level of generality, which does not qualify as integration into a practical application (Step 2A, prong II, see MPEP 2106.04(d)(2)). Furthermore, the additional elements recited are not significantly more because they simply append well-understood, routine, conventional activities previously known in the art (see MPEP 2106.05). Claims 24 and 25 are therefore rejected under 35 USC 101.
Regarding claims 26 and 29, claims 26 and 29 recites the judicial exceptions of claim 1 (Step 2A, prong I). Claim 26 further specifies that the sample is blood, plasma, or serum, and claim 29 recites that the subject is a heart transplant subject. However, recitation of the collection of a blood sample from a surgery patient simply amounts to a routine data-gathering step to determine the level of a biomarker and is therefore not integrated into a practical application because it is mere extra solution activity per MPEP 2106.05(g), “mere data-gathering step.” The additional limitations do not amount to significantly more than the recited judicial exceptions as such routine sample collection is routine in the art (MPEP 2106.05(d), section II).
Response to Arguments
The Applicant’s arguments filed 6/30/2025 have been considered but are not persuasive. The Applicant has amended independent claims 1 and 7 to now include steps of obtaining cell-free DNA and performing an assay to measure the amount of DS cf-DNA and total cf-DNA . The Applicant argues that such limitations are practical applications, and thus the claims are eligible at Step 2A, prong II of the subject matter eligibility analysis of the MPEP. However, recitation of these additional elements does not render a practical application onto the claims because the steps of obtaining DNA from a sample and measuring DNA in an assay simply amount to mere data gathering steps and extra solution activity, which is the proper analysis at step 2A, prong II. Additionally, given that the method steps are directed to measuring a biomarker in a subject, where information from the measurements are used as input into an equation, the additional claim limitations can also be viewed as extra-solution activity at Step 2A, prong II in the sense that MPEP 2106.05(g) states that “performing clinical tests on individuals to obtain input for an equation” is an example of mere extra-solution activity, as well as “determining the level of a biomarker in blood.” Thus, the present claims are not eligible at Step 2A, prong II of the Subject Matter Eligibility Test (MPEP 2106). The analysis of subject matter eligibility then proceeds to step 2B, which contrary to the Applicant’s assertion, does take into consideration the degree to which claim limitations are well-understood and routine (MPEP 2106.05(d)). Specifically, MPEP 2106.05(d) states that “determining the level of a biomarker in blood by any means,” “detecting DNA or enzymes in a sample,” “amplifying and sequencing nucleic acid sequences,” and “analyzing DNA to provide sequence information or detect allelic variants,” each of which is reasonably encompassed by an “assay” to measure the amount of DNA in the samples recited in claims 1 and 7, are all well-understood, routine, and conventional (MPEP 21006.05(d) section II). The recited claim limitations therefore do not amount to significantly more and fail the subject matter eligibility test at Step 2B. The claimed subject matter is therefore directed to judicial exceptions.
Claim Rejections - 35 USC § 112 – Updated in Response to Amendment
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 20-21 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.
Regarding claims 20-21, these claims recite “the time between samples” which lacks proper antecedent basis because1) no “time between samples” is mentioned in the claim or preceding claims and 2) only one sample is recited in the claim from which claims 20-21 depend (claim 7). It is unclear to what “samples” (plural) are being referenced.
Claim Rejections - 35 USC § 102 – Updated in Response to Amendment
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3, 5-9, 13, 17-26, and 29 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Beck (US 11,155,872 B2, original publication date of US 2018/0346982 A1 12/6/2018).
Regarding claim 1, Beck is a patent document that teaches a method of evaluating cell-free DNA in transplant patients (Title, Abstract, and see document). Beck teaches a method of assessing a sample from a transplant subject, the method comprising determining the product of an amount of donor-specific cell-free DNA (called “GcfDNA” in Beck) and an amount of total cf-DNA in the sample (column 20, third paragraph). Beck teaches: “the GcfDNA was the[sic] calculated by multiplying the GcfDNA [ % ] with the cfDNA [cp/mL] divided by the extraction efficiency of the internal standard,” (column 20, third paragraph). Beck therefore teaches “determining a product” of an amount of donor-specific cell free DNA and an amount of total cell-free DNA because the calculation taught by Beck involves multiplying DS cf-DNA and cell-free DNA, which is broadly encompassed by the claim. Beck teaches reporting and or recording the product (e.g., Figure 6). Furthermore, Beck teaches obtaining cf-DNA from a sample and performing an assay to determine the amount of donor specific DNA (column 20, fourth paragraph) and an amount of total cf-DNA in a sample (column 20, lines 19-22). Beck also teaches that the calculation of graft cf-DNA is used in their methods to analysis the status of transplant patients (e..g, Example 4).
Regarding claim 2, Beck teaches determining GcfDNA products at different points in time (column 4, second paragraph).
Regarding claim 3, Beck teaches determining one or more further products (i.e., GcfDNA measurements, per Beck) from samples taken from the subject monthly or bimonthly (column 11, third paragraph).
Regarding claim 5, Beck teaches comparing product values (i.e., GcfDNA, per Beck) to prior time points (e.g., Figures 9 and 10 of Beck teach a time course study which shows prior GcfDNA values plotted over time).
Regarding claim 6, Beck teaches that the percentage of GcfDNA can indicate complications/organ rejection (i.e., risks) when compared to a threshold (“the mean, typically 2SD,” column 11, third paragraph).
Regarding claim 7, Beck teaches obtaining cf-DNA from a sample and performing an assay to determine the amount of donor specific DNA (column 20, fourth paragraph) and an amount of total cf-DNA in a sample (column 20, lines 19-22). Beck teaches that their methods are to be used to detect cfDNA in a transplant patient (Abstract and throughout). Beck teaches a method of assessing a sample from a transplant subject, the method comprising determining the product of an amount of donor-specific cell-free DNA (called “GcfDNA” in Beck) and an amount of total cf-DNA in the sample (column 20, third paragraph). Beck teaches: “the GcfDNA was the[sic] calculated by multiplying the GcfDNA [ % ] with the cfDNA [cp/mL] divided by the extraction efficiency of the internal standard,” (column 20, third paragraph). Beck therefore teaches “determining a product” of an amount of donor-specific cell free DNA and an amount of total cell-free DNA because the calculation taught by Beck involves multiplying DS cf-DNA and cell-free DNA, which is broadly encompassed by the claim.
Beck teaches that GcfDNA analysis can be used to adjust treatment regimens, where determining such treatment is accomplished by monitoring multiple cfDNA samples taken over time (e.g., column 12, second paragraph). Beck also teaches that the calculation of graft cf-DNA is used in their methods to analysis the status of transplant patients (e.g. Example 4).
Regarding claim 8, Beck teaches obtaining samples from multiple timepoints (column 12, second paragraph).
Regarding claim 9, Beck teaches that sampling can be performed every two weeks (i.e., bimonthly, column 12, second paragraph).
Regarding claim 13, Beck teaches recording results because the document itself is a record of the experiments conducted (e.g., see Figures). Furthermore, Beck teaches long-term monitoring of patients as well as results from patient samples; a practitioner of ordinary skill could therefore at once envision that such results – which deal with critical patient medical information – could be formulated into a report (column 12, second and third paragraphs). Furthermore, Beck teaches that information obtained from biomarker analysis can be stored in a computer, which reasonably can be interpreted to be a database (column 12, fourth paragraph).
Regarding claim 17, Beck teaches that a product value (“GcfDNA,” per Beck) is associated with an increased risk when over a threshold (column 11, third paragraph).
Regarding claim 18, Beck teaches that a rise in GcfDNA in a sample is indicative of rejection as compared with “uncomplicated courses,” (column 11, third paragraph). Thus, Beck teaches that lower GcfDNA values are associated with less risk (i.e., “uncomplicated courses”).
Regarding claim 19, Beck teaches that monitoring regimens can be varied over a desired period of time depending on cfDNA counts (paragraph 12, second paragraph).
Regarding claims 20 and 21, Beck teaches that monitoring can be performed “at desired intervals,” (paragraph 12, second paragraph). Given that Beck also teaches that an increase in GcfDNA is associated with negative outcomes, a practitioner could immediately envision that sample monitoring times could be decreased if an increased medical risk is present in a patient (column 11, third paragraph). Similarly, regarding claim 21, a practitioner could at once envision increased time between sample monitoring if a decreased risk is present (column 11, third paragraph through column 12).
Regarding claim 22, Beck teaches additional testing to be conducted during monitoring in conjunction with GcfDNA monitoring (e.g., bilirubin and AST biomarker testing, Figure 5).
Regarding claim 23, Beck teaches that their methods are used to adjust treatment of a patient (column 3, fourth paragraph, column 12, second paragraph).
Regarding claim 24, Beck teaches treating a subject (column 12, third paragraph, column 4, fourth paragraph).
Regarding claim 25, Beck teaches adjusting an administrative schedule or dosage or one or more drugs (column 4, fourth paragraph). Given that Beck teaches that the administrative schedule of a drug is changed, it is reasonable to say that Beck teaches providing information about a treatment to a subject, who would be made aware of the administrative schedule change of the drug (column 4, fourth paragraph).
Regarding claim 26, Beck teaches that the sample can be a blood sample (column 11, third paragraph).
Regarding claim 29, Beck teaches the subject can be a heart transplant subject (column 17, second paragraph).
Response to Arguments
The Applicant’s arguments filed 6/30/2025 have been considered but are not persuasive. The Applicant argues that the amended claims are not anticipated by Beck because they contain limitations not taught and arranged in the same order as Beck. The Applicant argues that, in particular, Beck teaches multiplying graft cf-DNA with total cf-DNA and dividing by the extraction efficiency to determine total gf cf-DNA, while the present claims are directed to the product of donor-specific DNA and total cf-DNA as part of a method to assess a sample from a transplant patient. These arguments are not persuasive because 1) Beck’s method does involve the determination of a product of graft cf-DNA (i.e., donor-specific DNA) and total cf-DNA in order to determine a value of DS cf-DNA and 2) Beck’s methods are also directed to a method of assessing a sample from a transplant patient where DS cf-DNA (“graft” cf-DNA) is used as the biomarker (Abstract, Claims, and throughout). Thus, the elements of the amended claims are taught and anticipated by Beck.
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 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.
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/D.C.R./Examiner, Art Unit 1635
/KIMBERLY CHONG/Primary Examiner, Art Unit 1636