DETAILED ACTION
Applicant’s response, filed 02 March 2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 02 March 2026 has been entered.
Status of Claims
Claims 2, 8-13, and 15-158 are canceled.
Claim 159 is newly added.
Claims 1, 3-7, 14, and 159 are pending.
Claims 1, 3-7, 14, and 159 are rejected.
Priority
The effective filing date for the instant application is 19 April 2012.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 02 March 2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered by the examiner.
Claim Rejections - 35 USC § 101
The rejection of claims 2 and 12 under 35 U.S.C. 101 in the Office action mailed 28 Jan. 2025 has been withdrawn in view of the cancellation of these claims received 02 Mach 2026.
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, 3-7, 14, and 159 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and/or law of nature without significantly more. Any newly recited portion is necessitated by claim amendment.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claim 1 being representative) is directed to a method of analyzing nucleic acids in a subject. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim 1 recites the following steps which fall under the mathematical concepts and/or mental processes groupings of abstract ideas.
identifying a plurality of loci in the cf-DNA, the cfDNA comprising first nucleic acids of the subject and second nucleic acids of the transplant;
determining an allele of each of the plurality of loci;
selecting at least one informative locus from the plurality of loci based on the determining of the allele;
calculating an estimated allele frequency of a first allele at the at least one informative locus using a statistical distribution’
determining an amount of cfDNA of the transplant in the cf-DNA based on the estimated allele frequency;
comparing the amount of cf-DNA of the transplant to a threshold of 1%; and
determining a risk associated with the transplant in the subject based on whether the amount of cf-DNA of the transplant is equal to or exceeds the threshold value.
The identified claim limitations falls into one of the groups of abstract ideas of mental processes. First, identifying a plurality of loci in the cf-DNA can be practically performed in the mind by selecting a set of loci of interest (e.g. that had high amplification). Determining an allele at each locus involves analyzing the reads of each particular locus to determine an allele present at each locus. Selecting an informative locus from the loci involves selecting an allele that is homozygous at a particular locus. Calculating an estimated allele frequency using a statistical distribution involves determining a distribution of reads containing one of two alleles and determining a likely allele frequency of the first allele based on the distribution. Determining an amount of cell-free DNA of the transplant can be performed mentally by determining the allele frequency of the informative locus deviates from an expected allele frequency assuming no non-native nucleic acid is present to estimate an amount of non-native/transplant nucleic acid. The step of comparing the amount to a threshold amounts to a simple comparison of numbers, which can be practically performed in the mind. Last, determining a risk associated with the transplant can be practically performed in the mind by determining the subject is at high risk of the amount exceeds the threshold value. Therefore, nothing in the claims precludes the steps from being practically performed in the mind. See MPEP 2106.04(a)(2) III.
The limitations of calculating an estimated allele frequency of a first allele using a statistical distribution further recite a mathematical concept. A claim that recites a mathematical calculation, when the claim is given its broadest reasonable interpretation in light of the specification, will be considered as falling within the "mathematical concepts" grouping. A See MPEP 2106.04(a)(2) I. C. In the instant case, calculating an allele frequency of an allele, using a statistical distribution, amounts to a textual equivalent to performing mathematical calculations to calculate a numerical value. See MPEP 2106.04(a)(2) I. B. Therefore, these limitations recite a mathematical concept.
The claims further recite the law of nature of a natural correlation between an amount of non-native/transplant cell-free DNA present in a subject and an amount of risk associated with the transplant in the subject. See MPEP 2106.04(b) I.
Dependent claims 3-7, 14, and 159 further recite an abstract idea and/or are part of the abstract idea of claim 1. Claims 3-7 further limit the mental process of determining the risk to be a risk associated with the transplant, including an injury to the transplant that is initial or ongoing and a severity of the injury for claims 3-5, and to be a risk of having systemic disease, including inflammation, infection, or sepsis in claims 6-7. Dependent claim 14 further recites the mental process of detecting the first and second allele at a locus (i.e. analyzing sequencing data at a locus), and determining whether the first nucleic acids are homozygous for the second allele and the second nucleic acids are heterozygous or homozygous for the first allele at the at least one informative locus. Dependent claim 159 further recites the mental process of providing information about a therapy to the recipient of the transplant based on the determined risk. Therefore, claims 1, 3-7, 14, and 159 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 3-7 and 14 recite an abstract idea, as discussed above, but do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional element of claim 1 includes:
extracting cf-DNA from a biological sample obtained from the subject within 60 days of receiving a transplant; and
preparing the cf-DNA by performing PCR amplification on the extracted cf-DNA.
The additional element of claim 159 includes:
administering a therapy…to the recipient of a transplant based on the determined risk.
The additional elements of extracting cell-free DNA from the biological sample, preparing the cfDNA by performing PCR amplification on the extracted cf-DNA, and physically analyzing the DNA only serves to collect information for analysis by the abstract idea, which amounts to insignificant extra-solution activity that does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
First, MPEP 2106.04(d)(2), states that examiners should keep in mind that in order to qualify as a "treatment" or "prophylaxis" limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. If the limitation does not actually provide a treatment or prophylaxis, e.g., it is merely an intended use of the claimed invention or a field of use limitation, then it cannot integrate a judicial exception under the "treatment or prophylaxis" consideration. In the instant case, the step of administering is not required by the claim because claim 159 requires either administering a therapy OR providing information about a therapy, but not both.
Second, the treatment or prophylaxis limitation must be "particular," i.e., specifically identified so that it does not encompass all applications of the judicial exception(s). See MPEP 2106.04(d)(2) a.. In the instant case, even if the administering step was required, claim 159 only recites “administering a therapy…based on the determined risk”, which is analogous to the non-particular treatment of "administering a suitable medication to a patient” exemplified in MPEP 2106.04(d)(2) a.
Last, the treatment is simply administered “based on the determined risk”, which encompasses administering a therapy even if the subject was determined to have 0 risk. Therefore, the limitation also has an insignificant relationship with the judicial exception of determining the risk. Therefore the claims do not integrate the recited judicial exception into the practical application of affecting a particular treatment, and instead the additional element amount to mere instructions to apply the exception. See MPEP 2106.05(f).
Therefore, the additionally recited elements amount to mere instructions to apply the exception and/or insignificant extra-solution activity, and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1, 3-7, 14, and 159 are directed to an abstract idea and law of nature. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception for the following reasons.
Dependent claims 3-7 and 14 recite an abstract idea, as discussed above, but do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
he additional element of claim 1 includes:
extracting cf-DNA from a biological sample obtained from the subject within 60 days of receiving a transplant; and
preparing the cf-DNA by performing PCR amplification on the extracted cf-DNA.
The additional element of claim 159 includes:
administering a therapy…to the recipient of a transplant based on the determined risk.
The additional elements of extracting cell-free DNA from a biological sample, performing PCR on the extracted cf-DNA, and analyzing the physical cf-DNA are well-understood, routine, and conventional. This position is supported by Applicant’s specification, which discloses at pg. 16, para. 1 that cf-DNA can be extracted from a biological sample using any method known in the art, citing a plurality of commercially available extraction kits. Applicant’s specification at pg. 28, para. 3 and pg. 38, para. 3 similarly discloses commercially available kits to perform PCR on cf-DNA. With further respect to performing PCR to physically analyze the cf-DNA, the courts have also found the following laboratory techniques as well-understood, routine, and conventional: using polymerase chain reaction to amplify and detect DNA, 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); detecting DNA in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017); and amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014).
The additional elements of administering a therapy to the subject in claim 159 is not sufficient to provide significantly more and are well-understood, routine, and conventional. First, the administration step is not sufficient to provide significantly more because it is not required under the broadest reasonable interpretation of the claim as discussed above under Step 2A, Prong 2. Furthermore, even if the administration were required in claim 159, Applicant’s specification at pg. 20, para. 3 to pg. 21, para. 2 discloses therapies can include anti-rejection therapies and these therapies are known to those of ordinary skill in the art. Applicant’s specification at pg. 21, para. 3 further discloses administration of treatment or therapy may be accomplished by any method or known in the art and that compositions for different routes of administration are well known in the art.
Last, Sharma et al. (Mass spectrometric based analysis, characterization and applications of circulating cell free DNA isolated from human body fluids, 2011, International Journal of Mass Spectrometry, 304, pg. 172-183; newly cited) reviews the application of circulating cell-free DNA as a clinical diagnostic tool (Abstract). Sharma discloses hundreds of papers have been published on circulating cell-free DNA (pg. 172, col. 2, para. 2 to pg. 173, col. 1, para. 1) in addition to various studies analyzing cell-free DNA in transplant recipients (pg. 173, col. 1, para. 4 and col. 2, para. 4; Table 2), and further discusses cell-free DNA as biomarkers for organ transplantation (pg. 172, col. 1, para. 1; pg. 181, col. 2, para. 2). Sharma further discloses there has been considerable progress in understanding cell-free DNA through the use of the polymerase chain reaction technique, citing numerous studies that analyze cell-free DNA using PCR (Abstract; pg. 2, para. 2-3). Accordingly, even considering the additional elements in combination, extracting cell-free DNA and performing PCR on cell-free DNA in a clinical diagnosis context is well-understood, routine, and conventional.
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and natural correlation without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 02 March 2026 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks that claim 1 has been amended to be directed to a method of measuring cell-free DNA (cf-DNA) in a sample from a subject who is the recipient of a transplant, the method comprising extracting cf-DNA, preparing the cfDNA and determining the amount of cf-DNA with specific steps that are much more than mental steps (Applicant’s remarks at pg. 6, para. 4 to pg. 7, para. 1). Applicant further remarks the fact pattern in the present case is analogous to Illumina v. Ariosa Diagnostic because the instant claims are directed to methods for measuring cf-DNA (Applicant’s remarks at pg. 5, para. 3 to pg. 6, para. 1).
This argument is not persuasive. First, the step of “determining an amount of cf-DNA of the transplant based on the estimated allele frequency” is part of the abstract idea, involving analyzing estimated allele frequencies to quantify an amount of cf-DNA, as discussed in the above rejection, and therefore is not an additional element that may integrate the recited judicial exception into a practical application. While the steps of “extracting cf-DNA…” and “preparing the cfDNA by performing PCR amplification…” are additional elements, these additional limitations only serve to collect data for use by the abstract idea of determining the risk associated with the transplant, which is not sufficient to integrate the recited judicial exception into a practical application as set forth in MPEP 2106.05(g). Because the claims do not recite additional elements that integrate the recited judicial exception into a practical application, the claims are directed to the abstract idea under Step 2A, Prong 2.
Furthermore, the instant claims are not analogous to the claims in Illumina v. Ariosa Diagnostic, because the claims in Illumina v. Ariosa Diagnostic did not recite an abstract idea at all, and instead only recite limitations that physically prepare a DNA sample. While the instant claims do involve steps that prepare a cf-DNA sample, these limitations only serve to collect data for use by the abstract idea of determining the transplant risk in the subject. Therefore, unlike the claims in Illumina v. Ariosa Diagnostic, the instant claims are directed to an abstract idea. Furthermore, the additional elements for preparing the cf-DNA sample in the instant claims are conventional, as discussed under Step 2B above, and thus also do not provide significantly more than the judicial exception.
Claim Rejections - 35 USC § 102
The rejection of claims 1-5, 12, and 15 under 35 U.S.C. 102(b) in the Office action mailed 28 Jan. 2025 has been withdrawn in view of claim amendments and cancellations received 02 March 2026.
Applicant's arguments filed 02 March 2026 regarding 35 U.S.C. 102 have been fully considered and are persuasive. Synder does not explicitly teach the determination of a risk associated with the transplant based on whether the amount of cf-DNA is equal to or exceeds a threshold of 1% in a sample obtained from the subject. However, after further consideration of Synder, the limitation is considered obvious in view of Synder as applied in the new grounds of rejection set forth below.
Claim Rejections - 35 USC § 103
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.
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1, 3-5, 14, and 159 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Synder (2011). This rejection is newly recited and necessitated by claim amendment.
Cited reference: Synder et al., Universal noninvasive detection of solid organ transplant rejection, 2011, PNAS, 108(15), pg. 6229-6234; cited in IDS filed 06 March 2023 (previously cited)
Regarding claim 1, Snyder discloses a method for detecting transplant rejection in a subject (Abstract), which comprises the following steps:
Snyder discloses analyzing cell-free DNA extracted from blood samples obtained from a subject, wherein the analyzing comprises performing PCR on the extracted cell-free DNA to prepare the cf-DNA, to identify a plurality of loci (FIG. 1; pg. 6229, col. 1, para. 2-3; pg. 6232, col. 1, para. 2, e.g. 25,000 SNP containing reads; pg. 6234, col. 2, para. 3, e.g. sequencing uses PCR for library preparation). Synder further discloses the blood samples were obtained from the subject 14 days and also 1 month after a transplant (i.e. within 60 days of receiving the transplant) (pg. 6234, col. 1, para. 3, e.g. plasma samples taken 14 days post transplant; Figure 4, e.g. first point before 1 month).
Synder discloses identifying a plurality of loci in the cf-DNA (pg. 6232, col. 1, para. 1-2, wherein the DNA (i.e. nucleic acids) comprise nucleic acids native to the subject and non-native donor (i.e. transplant) DNA (i.e. the first and second nucleic acids) (pg. 6299, col. 1, para. 3; pg. 6234, col. 2, para. 2; Figure 1).
Snyder discloses determining an allele of each locus (pg. 6234, col. 2, para. 3, e.g. reads aligned to reference to identify alleles at each SNP site).
Snyder discloses selecting informative loci where the subject has a homozygous SNP in both alleles (i.e. based on the determined allele) (pg. 6231, col. 1, para. 4 to col. 2, para. 1, e.g. "each usable SNP…").
Snyder discloses calculating an allele frequency of an allele of each informative locus (i.e. a first allele at the at least one informative locus), based on counting a number of reads that falls into recipient, donor, or error bins (i.e. using a statistical categorical distribution) (pg. 6231, col. 1, para. 3 to col. 2, para. 3; Fig. S3, e.g. 2NAB--(B)/(NAB(A) + NAB(B) + NBB(A) NBB(B)).
Snyder discloses determining a percentage of donor DNA (i.e. an amount of transplant cf-DNA in the cell-free DNA) based on the estimated allele frequency of the informative loci (pg. 6231, col. 2, para. 3, e.g. counts used to calculate donor percentages; Figure 1).
Synder discloses comparing the amount of donor cell-free DNA in the subject to a threshold value (pg. 6230, col. 1, para. 2, to col. 2, para. 1, e.g. 2.0% donor DNA threshold captures 80% true positive rate; 6233, col. 1, para. 2, e.g. donor DNA levels used to indicate organ rejection; FIG. 4).
Snyder discloses determining a risk of organ rejection (i.e. a risk associated with the transplant) in the subject based on comparing the amount of donor cell-free DNA in the subject to the threshold value (pg. 6230, col. 1, para. 2, to col. 2, para. 1, e.g. 2.0% donor DNA threshold captures 80% true positive rate; 6233, col. 1, para. 2, e.g. donor DNA levels used to indicate organ rejection; FIG. 4).
Further regarding claim 1, Synder does not explicitly disclose the threshold value is 1%.
However, Synder discloses plotting a receiver operating curve (ROC) on the basis of different threshold for the donor DNA level, and discloses that at a threshold of 2.0% donor DNA, an 80% true positive rate with a 15% false positive rate was captured, while at a threshold of 1.7% donor DNA, an 83% true positive rate with a 16% false positive rate was captured (pg. 6230, col. 1, para. 2 to col. 2, para. 1; pg. 6232, col. 2, para. 3). Synder further discloses that donor DNA less than 1% and typically around 0.5% appear “normal” for heart transplant recipients and higher values are likely indicative of organ damage (pg. 6230, col. 2, para. 1), thus suggesting that donor DNA greater or equal to 1% is indicative of organ damage.
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the 2.0% or 1.7% threshold of Synder to have used a 1.0% threshold through routine experimentation of the threshold within the prior art conditions of increasing the threshold to reduce the false positive rate, while decreasing the threshold to increase the true positive rate, as demonstrated by Synder above, given Synder discloses donor DNA greater or equal to 1% is indicative of organ damage. See MPEP 2144.05 II. A.
Regarding the dependent claims:
Regarding claim 3, Synder further discloses the risk is a risk of organ rejection (i.e. a risk associated with the transplant, including a risk of transplant rejection) (pg. 6233, col. 1, para. 1).
Regarding claim 4, Synder discloses the risk associated with the transplant is a risk of transplant, as discussed above for claim 3, and the claims do not require that the risk associated with the transplant is a risk of injury to the transplant, including that the injury to the transplant is initial or ongoing. Therefore, claim 4 is rejected for the same reasons discussed for claim 3.
Regardless, Synder discloses assessing the risk of transplant rejection (i.e. also a transplant injury) months after transplantation (i.e. the injury is ongoing) (Fig. 2B and 2C; Fig. 4).
Regarding claim 5, Synder discloses the risk of transplant rejection (i.e. injury) is indicative of a severity of the injury, including “close to rejection” or “at rejection” (Fig. 4, e.g. higher % Donor DNA indicates more severe injury, see peak labeled Grade 3A rejection).
Regarding claim 14, Synder discloses selecting the at least one informative locus by determining alleles at SNP sites (i.e. a first and second allele at a locus) (pg. 6234, col. 2, para. 3; pg. 6231, col. 1, para. 4); and
Synder discloses determining the informative loci comprises determining SNP sites where the recipient has a homozygous allele (i.e. determining the first nucleic acids are homozygous for the second allele) that differs from the donor's genotype (i.e. the second nucleic acids are heterozygous or homozygous for the first allele, different than the second allele) (pg. 6234, col. 2, para. 3).
Regarding claim 159, Synder does not explicitly disclose administering a therapy to the subject based on the determined risk.
However, Snyder discloses treating the subject with an anti-rejection therapy based on a subject being at risk for organ rejection (e.g. as determined through a biopsy) (pg. 6231, col. 1, para. 2; pg. 6233, col. 1, para. 1; Abstract). Snyder further discloses the amounts of donor-derived DNA in plasma is a promising biomarker for the onset of organ rejection and that the level of donor DNA declines following treatment (pg. 6233, col. 1, para. 1). Snyder further discloses using amounts of donor-DNA as a biomarker provides a noninvasive test that replaces endomycocardial biopsy in heart transplant recipients (Abstract).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Snyder to have administered an anti-rejection therapy that treats inflammation based on the determined risk of transplant rejection, given Snyder discloses the level of donor DNA declines following treatment and suggests using the amount of donor-derived DNA as a biomarker for organ rejection in place of biopsies (pg. 6233, col. 1, para. 1). One of ordinary skill in the art would have been motivated to apply the determined amount of donor DNA to determine to administer an anti-rejection therapy to the subject to provide a non-invasive test for determining a risk of transplant rejection, as shown by Snyder (Abstract). This modification would have had a reasonable expectation of success given Snyder discloses treating a subject at risk for organ rejection and that an amount of DNA can be used as a biomarker for the risk of organ rejection (pg. 6231, col. 1, para. 2; pg. 6233, col. 1, para. 1; Abstract).
Therefore the invention is prima facie obvious.
Claims 6-7 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Synder (2011), as applied to claim 1 above, further in view of Rocha (2003). Any newly recited portion is necessitated by claim amendment.
Cited reference: Rocha et al., Effector mechanisms in transplant rejection, 2003, Immunol Rev., 196, pg. 51-64; previously cited.
Regarding claims 6-7, Synder further discloses the subject is a recipient of a transplant (Abstract) and that the risk is a risk of organ rejection (i.e. a risk associated with the transplant, including a risk of transplant rejection) (pg. 6233, col. 1, para. 1).
Further regarding claims 6-7, Synder does not disclose the risk associated with the transplant is a risk of having or developing systemic disease, wherein the systemic disease is inflammation, infection, or sepsis.
However, Rocha overviews mechanisms in transplant rejection (Abstract), and discloses that transplant rejection triggers inflammatory mediators that contribute to the pathogenesis of transplant rejection (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1), and that various inflammatory responses, including pro-inflammatory T-cell response (pg. 54, col.2 , para. 2), leukotrienes response (pg. 56, col. 2, para. 3), and complement pathway activation (pg. 57, col. 2, para. 2).
It would have been prima facie obvious to one of ordinary skill in the art, before the time of the invention, to have modified determined a risk of transplant rejection in the subject based on the determined amount of donor DNA of Synder, to have determined a risk of inflammation in the subject, given Rocha discloses that the mechanisms that cause organ transplant rejection also cause inflammation (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1; pg. 54, col. 2, para. 2; pg. 56, col. 2, para. 3; pg. 57, col. 2, para. 2). One of ordinary skill in the art would have been motivated to combine the method of Synder and Rocha based on the simple substitution of the risk of transplant rejection in Synder with the systemic disease of inflammation of Rocha, given Rocha discloses that the mechanisms that cause organ transplant rejection also cause inflammation (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1; pg. 54, col. 2, para. 2; pg. 56, col. 2, para. 3; pg. 57, col. 2, para. 2). Therefore, one of ordinary skill in the art would have been able to substitute the determining the risk of systemic disease of transplant rejection with the systemic disease of inflammation, and the results of the substitution would have been predictable given Rocha discloses inflammation occurs with transplant rejection, as discussed above.
Therefore, the invention is prima facie obvious.
Response to Arguments
Applicant's arguments filed 02 March 2026 regarding 35 U.S.C. 103 have been fully considered but they are not persuasive.
Applicant remarks that Synder does not teach or suggest the method of claim 1, and Rocha does not remedy the deficiencies of Synder, and thus claims 6-7 are not obvious (Applicant’s remarks at pg. 6, para. 7 to pg. 7, para. 3).
This argument is not persuasive because it does not take into account the newly cited portions of Synder discussed in the new grounds of rejection of claim 1 under 35 U.S.C. 103. While Synder does not explicitly teach the recited 1% threshold, it would have been prima facie obvious to use a 1% threshold in view of Synder for the reasons discussed in the above rejection. Furthermore, Rocha is not relied upon to teach the threshold.
Double Patenting
The various rejections of claims 2 and 12 on the ground of nonstatutory double patenting in the Office action mailed 28 Jan. 2025 have been withdrawn in view of the cancellation of these claims received 02 March 2026.
The rejection of claims 1, 3-4, 6, and 14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US 10472680 B2 in the Office action mailed 28 Jan. 2025 have been withdrawn in view of claim amendments received 02 March 2026. However, a new grounds of rejection is set forth below in view of the claim amendments.
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.
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Claims 1, 3-6, 14, and 159 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US 10385396 B2 in view of Synder (2011). Any newly recited portion is necessitated by claim amendment.
Cited references:
Synder et al., Universal noninvasive detection of solid organ transplant rejection, 2011, PNAS, 108(15), pg. 6229-6234 and suppl. (cited in IDS; previously cited).
Regarding instant claim 1, reference claim 1 discloses analyzing nucleic acids from cell-free DNA extracted from a biological sample from a subject, wherein the cell-free DNA includes nucleic acids from the subject and non-native to the subject. Reference claim 4 discloses the method is performed within 30 days of receiving the transplant.
Reference claim 1 discloses determining an amount of cell-free DNA not native to the subject in the cell-free DNA.
Reference claim 1 discloses determining a risk in the subject based on the determined amount of cell-free DNA not native to the subject.
Reference claim 1 discloses administering an anti-rejection therapy or a therapeutic agent that treats a systemic disease to the subject based on the determined risk.
Regarding instant claims 3¸ reference claim 2 discloses the risk is a risk of transplant rejection (i.e. injury to the transplant).
Regarding instant claim 4, reference claims 3-7 disclose the method can be performed within 3 to 30 days of receiving the transplant, which demonstrates the risk can be an ongoing injury or an initial injury.
Regarding instant claim 6, reference claims 1 and 12 disclose administering an agent that treats systemic disease, when the determined amount of non-native cell-free DNA is greater than a threshold, which demonstrates the risk is for developing systemic disease.
Regarding instant claim 159, reference claim 1 discloses administering an anti-rejection therapy when the determined amount is greater than the threshold value (i.e. based on determined risk).
Further regarding instant claim 1 the reference claims do not disclose amplifying the cfDNA using PCR, that determining the amount of non-native cell-free DNA comprises identifying a plurality of loci, determining an allele of each of the plurality of loci, selecting at least one informative locus based on the determining of the allele, and calculating an estimated allele frequency of a first allele of the at least one informative locus based on a statistical distribution, or using a threshold value of 1%. Further regarding instant claim 14¸ the reference claims do not disclose determining the informative locus is by detecting the first allele and a second allele at a locus; and determining the first nucleic acids are homozygous for the second allele at the at least one informative locus and the second nucleic acids are heterozygous or homozygous for the first allele at the at least one informative locus. Further regarding instant claim 5, the reference claims do not disclose the risk is indicative of the severity of the injury.
However, Synder discloses analyzing cell-free DNA from blood samples obtained from a subject to identify a plurality of loci, comprising extracting cfDNA from blood samples and performing PCR to amplify the cfDNA (FIG. 1; pg. 6299, col. 1, para. 2-3; pg. 6232, col. 1, para. 2, e.g. 25,000 SNP containing reads), wherein the DNA (i.e. nucleic acids) comprise nucleic acids native to the subject and non-native donor DNA (i.e. the first and second nucleic acids) (pg. 6299, col. 1, para. 3; Figure 1). Synder discloses determining an allele of each locus (pg. 6234, col. 2, para. 3, e.g. reads aligned to reference to identify alleles at each SNP site). Synder discloses selecting informative loci where the subject has a homozygous SNP in both alleles (i.e. based on the determined allele) (pg. 6231, col. 1, para. 4 to col. 2, para. 1, e.g. "each usable SNP…"). Synder discloses calculating an allele count of an allele of each informative locus (i.e. a first allele at the at least one informative locus), based on counting a number of reads that falls into recipient, donor, or error bins (i.e. using a statistical categorical distribution) (pg. 6231, col. 2, para. 1-3; Fig. S3). Synder discloses selecting the at least one informative locus by determining alleles at SNP sites (i.e. a first and second allele at a locus) (pg. 6234, col. 2, para. 3; pg. 6231, col. 1, para. 4); and determining the informative loci comprises determining SNP sites where the recipient has a homozygous allele (i.e. determining the first nucleic acids are homozygous for the second allele) that differs from the donor's genotype (i.e. the second nucleic acids are heterozygous or homozygous for the first allele, different than the second allele) (pg. 6234, col. 2, para. 3). Synder discloses determining a percentage of donor DNA (i.e. an amount of cell-free DNA not native to the subject in the cell-free DNA) based on the estimated allele frequency of the informative loci (pg. 6231, col. 2, para. 3, e.g. counts used to calculate donor percentages; Figure 1), and that this percentage is used to determine a risk of organ rejection in the subject (pg. 6233, col. 1, para. 1, e.g. donor DNA levels used to indicate organ rejection). Synder further discloses the risk of transplant rejection (i.e. injury) is indicative of a severity of the injury, including “close to rejection” or “at rejection” (Fig. 4, e.g. higher % Donor DNA indicates more severe injury, see peak labeled Grade 3A rejection).
Synder further discloses plotting a receiver operating curve (ROC) on the basis of different threshold for the donor DNA level, and discloses that at a threshold of 2.0% donor DNA, an 80% true positive rate with a 15% false positive rate was captured, while at a threshold of 1.7% donor DNA, an 83% true positive rate with a 16% false positive rate was captured (pg. 6230, col. 1, para. 2 to col. 2, para. 1; pg. 6232, col. 2, para. 3). Synder further discloses that donor DNA less than 1% and typically around 0.5% appear “normal” for heart transplant recipients and higher values are likely indicative of organ damage (pg. 6230, col. 2, para. 1), thus suggesting that donor DNA greater or equal to 1% is indicative of organ damage.
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims with the method of determining an amount of non-native cell-free DNA in the subject of Synder (pg. 6299, col. 1, para. 3; Figure 1; pg. 6231, col. 1, para. 4 to col. 2, para. 1; pg. 67231, col. 1, para. 1-3; Fig. S3; pg. 6231, col. 2, para. 3), thus arriving at the inventions of the instant claims. One of ordinary skill in the art would have been motivated to combine the methods of the reference claims and Synder to have predicted a risk of transplant rejection with an 80% true positive rate (pg. 6230, col. 1, para. 2 to col. 2, para. 1). This modification would have had a reasonable expectation of success given both the reference claims and Synder utilize an estimated amount of non-native cell-free DNA in a subject to estimate a risk of systemic disease.
It would have been further prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the 2.0% or 1.7% threshold of Synder to have used a 1.0% threshold through routine experimentation of the threshold within the prior art conditions of increasing the threshold to reduce the false positive rate, while decreasing the threshold to increase the true positive rate, as demonstrated by Synder above, given Synder discloses donor DNA greater or equal to 1% is indicative of organ damage. See MPEP 2144.05 II. A.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US 10385396 B2 in view of Synder (2011), as applied to claim 6 above, and further in view of Rocha (2003). This rejection is previously recited.
Cited reference: Rocha et al., Effector mechanisms in transplant rejection, 2003, Immunol Rev., 196, pg. 51-64; previously cited.
Regarding instant claim 7, reference claims 1-12 in view of Synder disclose the method of instant claim 6 as applied above.
Further regarding instant claim 7, while the reference claims in view of Synder disclose determining a risk of transplant rejection, they do not disclose the risk is for a systemic disease of inflammation.
However, Rocha overviews mechanisms in transplant rejection (Abstract), and discloses that transplant rejection triggers inflammatory mediators that contribute to the pathogenesis of transplant rejection (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1), and that various inflammatory responses, including pro-inflammatory T-cell response (pg. 54, col.2 , para. 2), leukotrienes response (pg. 56, col. 2, para. 3), and complement pathway activation (pg. 57, col. 2, para. 2).
It would have been prima facie obvious to one of ordinary skill in the art, before the time of the invention, to have modified the determined a risk of transplant rejection in the subject based on the determined amount of donor DNA of the reference claims in view of Synder, to have determined a risk of inflammation in the subject, given Rocha discloses that the mechanisms that cause organ transplant rejection also cause inflammation (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1; pg. 54, col. 2, para. 2; pg. 56, col. 2, para. 3; pg. 57, col. 2, para. 2). One of ordinary skill in the art would have been motivated to combine the method of the reference claims in view of Synder and Rocha based on the simple substitution of the risk of the systemic disease of transplant rejection in Synder with the systemic disease of inflammation of Rocha, given Rocha discloses that the mechanisms that cause organ transplant rejection also cause inflammation (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1; pg. 54, col. 2, para. 2; pg. 56, col. 2, para. 3; pg. 57, col. 2, para. 2). Therefore, one of ordinary skill in the art would have been able to substitute the determining the risk of systemic disease of transplant rejection with the systemic disease of inflammation, and the results of the substitution would have been predictable given Rocha discloses inflammation occurs with transplant rejection, as discussed above.
Claims 1, 3-6, 14, and 159 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US 10472680 B2 in view of Synder (2011). This rejection is newly recited and necessitated by claim amendment.
Cited reference: Synder et al., Universal noninvasive detection of solid organ transplant rejection, 2011, PNAS, 108(15), pg. 6229-6234 and suppl. (cited in IDS; previously cited).
Although the claims at issue are not identical, they are not patentably distinct from each other because:
It is noted that although the instant App. is a divisional of the reference application, the claims of the application under examination and claims of the other application/patent are not consonant with the restriction requirement made by the examiner, since the claims have been changed in material respects from the claims at the time the requirement was made. For example, the divisional application filed includes additional claims not consonant in scope with the original claims subject to restriction in the parent. Symbol Technologies, Inc. v. Opticon, Inc., 935 F.2d 1569, 19 USPQ2d 1241 (Fed. Cir. 1991); Gerber Garment Technology, Inc. v. Lectra Systems, Inc., 916 F.2d 683, 16 USPQ2d 1436 (Fed. Cir. 1990). Therefore, the prohibition against nonstatutory double patenting rejections under 35 U.S.C. 121 does not apply. See MPEP 804.01.
Regarding instant claim 1, reference claims 1 and 12 discloses the limitation of instant claim 1, except that reference claim 1 does not explicitly disclose extracting cf-DNA from a biological sample obtained within 60 days of a transplant, preparing the cf-DNA by performing PCR, or determining a risk associated with the transplant as claimed.
Regarding instant claim 5, the reference claims do not teach the risk is indicative of the severity of the injury.
However, Synder discloses analyzing cell-free DNA from blood samples obtained from a subject to identify a plurality of loci including extracting cell-free DNA and performing PCR (FIG. 1; pg. 6299, col. 1, para. 2-3; pg. 6232, col. 1, para. 2, e.g. 25,000 SNP containing reads), wherein the DNA (i.e. nucleic acids) comprise nucleic acids native to the subject and non-native donor DNA (i.e. the first and second nucleic acids) (pg. 6299, col. 1, para. 3; Figure 1). Synder discloses determining a percentage of donor DNA (i.e. an amount of cell-free DNA not native to the subject in the cell-free DNA) based on the estimated allele frequency of the informative loci identified in the analyzed cf-DNA (pg. 6231, col. 2, para. 3, e.g. counts used to calculate donor percentages; Figure 1), and that this percentage is used to determine a risk of organ rejection in the subject (pg. 6233, col. 1, para. 1, e.g. donor DNA levels used to indicate organ rejection). Synder further discloses the risk of transplant rejection (i.e. injury) is indicative of a severity of the injury, including “close to rejection” or “at rejection” (Fig. 4, e.g. higher % Donor DNA indicates more severe injury, see peak labeled Grade 3A rejection). Synder further discloses the risk of transplant rejection (i.e. injury) is indicative of a severity of the injury, including “close to rejection” or “at rejection” (Fig. 4, e.g. higher % Donor DNA indicates more severe injury, see peak labeled Grade 3A rejection), as recited in instant claim 5.
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims with the method of determining an amount of non-native cell-free DNA in the subject of Synder (pg. 6299, col. 1, para. 3; Figure 1; pg. 6231, col. 1, para. 4 to col. 2, para. 1; pg. 67231, col. 1, para. 1-3; Fig. S3; pg. 6231, col. 2, para. 3), thus arriving at the inventions of the instant claims. One of ordinary skill in the art would have been motivated to combine the methods of the reference claims and Synder to have predicted a risk of transplant rejection with an 80% true positive rate (pg. 6230, col. 1, para. 2 to col. 2, para. 1). This modification would have had a reasonable expectation of success given both the reference claims and Synder utilize an estimated amount of non-native cell-free DNA in a subject to estimate a risk of systemic disease.
Regarding instant claim 3, reference claim 1 discloses the treatment is an anti-rejection therapy, demonstrating the risk is of a rejection of the transplant.
Regarding instant claim 4¸ given reference claim 1 makes obvious determining the risk of a transplant rejection (i.e. a transplant injury), as applied to claim 3, the risk is inherently for either an initial rejection (i.e. the rejection has not happened yet) or ongoing (the rejection has already started).
Regarding instant claim 6, reference claim 1 discloses administering a therapeutic agent that treats a systemic disease when the determined amount of cell-free DNA not native to the subject is greater than a threshold, which demonstrates the risk is for systemic disease.
Regarding instant claim 12, reference claim 5 discloses analyzing the cell-free DNA uses sequencing, which would require the cell-free DNA is extracted from the sample.
Regarding instant claim 14, reference claim 2 discloses the limitations of instant claim 14.
Regarding instant claim 159, reference claim 1 discloses the administering of anti-rejection therapy when the determined amount is greater than a threshold.
Claim 7 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. US 10472680 B2 in view of Synder, as applied to instant claim 6 above, further in view Rocha (2003). Any newly recited portion is necessitated by claim amendment.
Cited reference: Rocha et al., Effector mechanisms in transplant rejection, 2003, Immunol Rev., 196, pg. 51-64; previously cited.
Regarding instant claim 7, reference claims 1-12 disclose the method of instant claim 6 as applied above.
Further regarding instant claim 7, the reference claims do not disclose the risk is for a systemic disease of inflammation.
However, Rocha overviews mechanisms in transplant rejection (Abstract), and discloses that transplant rejection triggers inflammatory mediators that contribute to the pathogenesis of transplant rejection (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1), and that various inflammatory responses, including pro-inflammatory T-cell response (pg. 54, col.2 , para. 2), leukotrienes response (pg. 56, col. 2, para. 3), and complement pathway activation (pg. 57, col. 2, para. 2).
It would have been further prima facie obvious to one of ordinary skill in the art, before the time of the invention, to have modified the determined a risk of transplant rejection in the subject based on the determined amount of donor DNA of the reference claims, to have determined a risk of inflammation (i.e. a systemic disease) in the subject, given Rocha discloses that the mechanisms that cause organ transplant rejection also cause inflammation (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1; pg. 54, col. 2, para. 2; pg. 56, col. 2, para. 3; pg. 57, col. 2, para. 2). One of ordinary skill in the art would have been motivated to combine the method of the reference claims in view of Synder and Rocha based on the simple substitution of the risk of the systemic disease of transplant rejection in Synder with the systemic disease of inflammation of Rocha, given Rocha discloses that the mechanisms that cause organ transplant rejection also cause inflammation (Abstract; pg. 55, col. 2, para. 3 to pg. 56, col. 1, para. 1; pg. 54, col. 2, para. 2; pg. 56, col. 2, para. 3; pg. 57, col. 2, para. 2). Therefore, one of ordinary skill in the art would have been able to substitute the determining the risk of systemic disease of transplant rejection with the systemic disease of inflammation, and the results of the substitution would have been predictable given Rocha discloses inflammation occurs with transplant rejection, as discussed above.
Claims 1, 3-7, 14, and 159 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-7, 13-14, 48, 104, and 159 of copending Application No. 16/504,469 (reference application) in view of Synder (2011). Any newly recited portion is necessitated by claim amendment.
Regarding instant claim 1, reference claim 1 discloses the limitations of instant claim 1, except that the sample is obtained within 60 days of the transplant. It is further noted reference claim 1 is narrower in scope given it requires the statistical distribution is a binomial distribution. However, reference claim 104 discloses determining the risk within 10 days of receiving the transplant, such that the sample is obtained within 10 days (i.e. within 60 days).
Regarding instant claims 3-7, 14, and 159, reference claims 3-7, 14, and 159 disclose the limitations of instant claims 3-7, 14, and 159 verbatim.
Response to Arguments
Applicant's arguments filed 08 May 2026 regarding double patenting have been fully considered but they are not persuasive.
Applicant remarks the Office has not established that the claims of the instant application are anticipated or rendered obvious by the claims of the above referenced patents and patent applications (Applicants’ remarks at pg. 7, para. 7 to pg. 8, para. 1).
This argument is not persuasive because Applicant's arguments fail to comply with 37 CFR 1.111(b) because they amount to a general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the referenced patents and/or patent applications.
Conclusion
No claims are allowed.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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