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 .
Claims Status
Claims 44, 45, 47, 49-53, 55, & 56 filed on 08/14/2026 are pending. The cancellation of claims 46, 48, & 54 without prejudice or disclaimer in the response filed on 08/14/2026 is acknowledged. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 101
Claims 50-53, 55, & 56 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural correlation/law of nature without significantly more. This judicial exception is not integrated into a practical application and the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons set forth below.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106. The unpatentability of abstract ideas was confirmed by the U.S. Supreme court in Bilski v. Kappos, 561 U.S. 593, 601 (June 28, 2010) and Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014). See also Myriad v Ambry, CAFC 2014-1361, -1366, December 17, 2014. The unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66, 71 (2012). “[L]aws of nature, natural phenomena, and abstract ideas” are not patentable. Dia-mond v. Diehr, 450 U. S. 175, 185 (1981); see also Bilski v. Kappos, 561 U. S. at 601 (2010).
Claims Analysis:
As set forth in MPEP 2106, the claims have been analyzed to determine whether they are directed to one of the four statutory categories (STEP 1).
The instant claims are directed to methods and therefore are directed to one of the four statutory categories of invention.
The claims are then analyzed to determine if they recite a judicial exception (JE) (STEP 2A, prong 1) [Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1293 (2012), Alice Corp. Pry. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347 (2014)].
The claimed invention recites a method for treating a transplant complication in a heart transplant recipient comprising extracting cell-free DNA from a biological sample from the heart transplant recipient, amplifying the cell-free DNA, analyzing and quantifying the amount of total cell-free DNA, and administering a treatment for a transplant complication if the total cell-free DNA is above a threshold total. This recitation is a natural correlation between transplant complication and total cell-free DNA. With regard to the natural correlation, as in Mayo, the relationship is itself a natural process that exists apart from any human action. It is therefore determined that the claims are directed to judicial exceptions.
The claims are then analyzed to determine whether they recite an element or step that integrates the JE into a practical application (STEP 2A, prong 2) [Vanda Pharmaceuticals Inc., v. West-Ward Pharmaceuticals, 887 F.3d 1117 (Fed. Cir. 2018)].
The claims recite steps of extracting cell-free DNA, performing PCR amplification, analyzing and quantifying total cell-free DNA, and administering a treatment, however this does not integrate the JE into a practical application because it is a mere data gathering step to use the correlation and does not add a meaningful limitation to the method.
Although the claims recite “administering a treatment” to the heart transplant recipient, this step is conditional as it is determined by total cell-free DNA being equal to or above a threshold total cell-free DNA value. Accordingly, these generally recited elements are considered nothing more than instructions to apply the law of nature because no particular conditions are required by the step of quantifying cfDNA. As such, the “administering” step is merely a generalized “treat” limitation with no particularity that integrates the judicial exception into a practical application. The Supreme Court does acknowledge that it is possible to transform an unpatentable law of nature, but one must do more than simply state the law of nature while adding the words "apply it.” CLS BankInt’l, 134 S.Ct. at 2358; Prometheus, 132 S. Cl, at 1294.
In the absence of steps or elements that integrate the JE into a practical application, the additional elements/steps are considered to determine whether they add significantly more to the JE either individually or as an ordered combination, to “’transform the nature of the claim’ into a patent eligible application” [Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S. Ct. 1289, 1293 (2012), Alice Corp. Pry. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347 (2014)] (STEP 2B).
In the instant situation, the steps of detecting total cell-free DNA through extraction, PCR amplification, and quantification, are generally recited and do not provide any particular reagents that might be considered elements that transform the nature of the claims into a patent eligible application because no specific elements/steps are recited. This step is not only a mere data gathering step, but the general recitation of detection of known nucleic acids is well understood, routine, and conventional activity (See MPEP 2106.05(d)(II)). Applicant is reminded that in Mayo, the Court found that “[i]f a law of nature is not patentable, then neither is a process reciting a law of nature, unless that process has additional features that provide practical assurance that the process is more than a drafting effort designed to monopolize the law of nature itself.” Further "conventional or obvious" "[pre]solution activity" is normally not sufficient to transform an unpatentable law of nature into a patent-eligible application of such a law”. Flook, 437 U. S., at 590; see also Bilski, 561 U. S., at ___ (slip op., at 14) (“[T]he prohibition against patenting abstract ideas ‘cannot be circumvented by’ . . . adding ‘insignificant post-solution activity’” (quoting Diehr, supra, at 191–192)). The Court also summarized their holding by stating “[t]o put the matter more succinctly, the claims inform a relevant audience about certain laws of nature; any additional steps consist of well understood, routine, conventional activity already engaged in by the scientific community; and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately.” Therefore these limitations/steps do not “‘transform the nature of the claim’ into a patent-eligible application.’” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
When viewed as an ordered combination, the claimed limitations are directed to nothing more than the determination that a natural correlation/phenomena exists. Any additional element consists of using well understood, routine and conventional activity, and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately.
Accordingly, it is determined that the instant claims are not directed to patent eligible subject matter.
Response to Arguments
The response traverses the rejection. The response asserts that the claims recite a specific, multi-step method for preparing a non-naturally occurring composition of amplified DNA and using that composition to guide clinical treatment decisions. Further, the response asserts that under step 1 of the Alice/Mayo analysis the claims are not directed to a judicial exception and instead the claims are directed to a practical method of treating transplant complications with steps (a)-(d) and that this specific technological process produces a new composition and uses the result to guide treatment, not a claim to a natural correlation. This argument has been thoroughly reviewed but was not found persuasive. First, step 1 analyzes the claims to determine whether they are directed to one of the four statutory categories in which the instant claims are directed to methods and therefore are directed to one of the four statutory categories of invention. Further, step 2A Prong 1 then analyzes the claims to determine whether a judicial exception is recited in which The claimed invention recites a method for treating a transplant complication in a heart transplant recipient comprising extracting cell-free DNA from a biological sample from the heart transplant recipient, amplifying the cell-free DNA, analyzing and quantifying the amount of total cell-free DNA, and administering a treatment for a transplant complication if the total cell-free DNA is above a threshold total. This recitation is a natural correlation between transplant complication and total cell-free DNA. With regard to the natural correlation, as in Mayo, the relationship is itself a natural process that exists apart from any human action. It is therefore determined that the claims are directed to judicial exceptions.
The response also asserts that the claims integrate any alleged judicial exception into a practical application under Step 2A, Prong 2 as the claims provide a specific treatment step, administering treatment for a transplant complication when the quantified total cfDNA equals or exceeds a threshold that transforms the claims into patent eligible subject matter. Further, the response asserts that this treatment step is not merely recited at a high level of generality but rather the claims specify a treatment for a transplant complication and further specify that the treatment is an anti-rejection or a cardia arrest treatment. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed above, although the claims recite “administering a treatment” to the heart transplant recipient, this step is conditional as it is determined by total cell-free DNA being equal to or above a threshold total cell-free DNA value. Accordingly, these generally recited elements are considered nothing more than instructions to apply the law of nature because no particular conditions are required by the step of quantifying cfDNA. As such, the “administering” step is merely a generalized “treat” limitation with no particularity that integrates the judicial exception into a practical application. The Supreme Court does acknowledge that it is possible to transform an unpatentable law of nature, but one must do more than simply state the law of nature while adding the words "apply it.” CLS BankInt’l, 134 S.Ct. at 2358; Prometheus, 132 S. Cl, at 1294. Further, anti-rejection treatment and cardiac arrest treatment is broad and encompassed a wide range of possible treatment and therefore not meaningful constraints on the administration such that a particular treatment consideration would apply because it is not limited to any particular anti-rejection or cardiac arrest treatment (see example 49 of 2024 Guidance Update on Patent Subject Matter Eligibility).
The response also asserts that even if the claims were to be found directed to a judicial exception, the claims recite significantly more that any alleged exception under Step 2B as the claimed method is not routine or conventional and instead recites an unconventional ordered combination of steps providing an inventive concept that amounts to significantly more that any alleged natural correlation. The response also asserts the experimental determination of clinically relevant threshold values is far from routine or conventional. This argument has been thoroughly reviewed but was not found persuasive as the steps of detecting total cell-free DNA through extraction, PCR amplification, and quantification, are generally recited and do not provide any particular reagents that might be considered elements that transform the nature of the claims into a patent eligible application because no specific elements/steps are recited. This step is not only a mere data gathering step, but the general recitation of detection of known nucleic acids is well understood, routine, and conventional activity (See MPEP 2106.05(d)(II)).
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Claim Rejections - 35 USC § 103
Claim(s) 44, 45, 49, 50-52, 55, & 56 is/are rejected under 35 U.S.C. 103 as being unpatentable over Vlaminck (Vlaminck et al.; Science Translational Medicine, Vol. 6, pages 1-9, June 2014), in view of Cha (Cha, Zarbl, Keohavong, & Thilly; PCR Methods and Applications, Vol. 2, pages 14-20, April 1992).
Regarding amended claim 44, Vlaminck teaches a noninvasive diagnostic method for high-throughput screening of circulating cell-free donor-derived DNA (non-naturally occurring composition of cell-free DNA) to measure acute rejection after heart transplantation through extracting cell-free DNA from whole-blood samples of the heart transplant recipient after transplant (biological sample), quantifying the cell-free DNA through quantitative PCR and sequencing (performing PCR amplification on the cell-free DNA and preparing a non-naturally occurring composition of amplified DNA), and analyzing the cell-free donor-derived DNA levels (analyzing the non-naturally occurring composition of amplified DNA by quantitative PCR to quantify an amount of total cf-DNA in the biological sample) (abstract lines 1-11; pg. 2 column 2 3rd full paragraph lines 1-15; pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-14; pg. 7 column 1 2nd full paragraph lines 1-16; pg. 7 column 2 3rd full paragraph lines 1-5; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 4). Vlaminck also teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2).
Vlaminck does not teach that the quantitative PCR comprises performing PCR with a first primer pair and a second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of SNV target but a 3’ double mismatch to a second allele of the SNV target.
Cha teaches a method of allele-specific PCR through the use of primers that have a single mismatch to the mutated allele at the 3’ end of the primer (first primer pair comprises a 3’ penultimate mismatch relative to a first allele of the SNV target) and a double mismatch with the wildtype allele (a double 3’ mismatch relative to a second allele of the SNV target) and primers to the wildtype allele with no mismatches (second primer pair specifically amplifies the second allele) (plurality of primer pairs to generate a plurality if amplicons) (abstract lines 1-17; pg. 14-15 paragraph bridging pg. 14 & 15 lines 1-21; Table 1). In addition, Cha teaches that this method achieve a sensitivity that enables measuring specific, infrequent mutations in samples (abstract lines 1-7).
Vlaminck and Cha are considered to be analogous to the claimed invention because they are all in the same field of use of amplification to detect single nucleotide variants. Therefore, 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 quantifying cell-free DNA using quantitative PCR in Vlaminck to incorporate the use of primer pairs in an amplification reaction comprising a primer pair comprising a primer with a 3’ single mismatch to a first allele and a 3’ double mismatch to a second allele and a primer pair for amplifying the second allele as taught in Cha because Cha teaches that doing so would provide a pairs of primers that achieve a sensitivity to enables measuring specific, infrequent mutations in samples.
Regarding amended claim 45, Vlaminck teaches plasma is extracted from whole blood samples to extract cell-free DNA (biological sample is blood or plasma) (pg. 7 column 2 3rd full paragraph lines 1-5).
Regarding claim 49, Vlaminck teaches a noninvasive diagnostic method for high-throughput screening of circulating cell-free donor-derived DNA (non-naturally occurring composition of cell-free DNA) to measure acute rejection after heart transplantation (transplant recipient is a heart transplant recipient) (abstract lines 1-11).
Regarding amended claim 50, Vlaminck teaches a noninvasive diagnostic method for high-throughput screening of circulating cell-free donor-derived DNA (non-naturally occurring composition of cell-free DNA) to measure acute rejection after heart transplantation through extracting cell-free DNA from whole-blood samples of the heart transplant recipient after transplant (biological sample), quantifying the cell-free DNA through quantitative PCR and sequencing (performing PCR amplification on the cell-free DNA and preparing a non-naturally occurring composition of amplified DNA), and analyzing the cell-free donor-derived DNA levels (analyzing the non-naturally occurring composition of amplified DNA by quantitative PCR to quantify an amount of total cf-DNA in the biological sample) (abstract lines 1-11; pg. 2 column 2 3rd full paragraph lines 1-15; pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-14; pg. 7 column 1 2nd full paragraph lines 1-16; pg. 7 column 2 3rd full paragraph lines 1-5; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 4). Vlaminck also teaches that this method of measuring the levels of the cell-free donor-derived DNA in heart transplant recipients provide an opportunity to diagnose and treat acute rejection through chosen threshold values to maximize sensitivity or specificity of the quantified cell-free donor-derived DNA (administering a treatment for a transplant complication to the heart transplant recipient provided the total cf-DNA in the biological sample is equal to or above a threshold total) (pg. 6 column 2 1st full paragraph lines 1-12). Finally, Vlaminck teaches that cell-free donor-derived DNA levels in the heart transplant recipients with acute rejection (transplant complication) are at levels up to 10% (in which percent concentration represents g/100mL, therefore 10g/100mL (0.1g/mL) = 0.1 = 10% and further converted from g/mL to ng/mL which is equal to 100,000,000 ng/mL) (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (Fig.4C). Vlaminck also teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2).
Vlaminck does not teach that the quantitative PCR comprises performing PCR with a first primer pair and a second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of SNV target but a 3’ double mismatch to a second allele of the SNV target.
Cha teaches a method of allele-specific PCR through the use of primers that have a single mismatch to the mutated allele at the 3’ end of the primer (first primer pair comprises a 3’ penultimate mismatch relative to a first allele of the SNV target) and a double mismatch with the wildtype allele (a double 3’ mismatch relative to a second allele of the SNV target) and primers to the wildtype allele with no mismatches (second primer pair specifically amplifies the second allele) (plurality of primer pairs to generate a plurality if amplicons) (abstract lines 1-17; pg. 14-15 paragraph bridging pg. 14 & 15 lines 1-21; Table 1). In addition, Cha teaches that this method achieve a sensitivity that enables measuring specific, infrequent mutations in samples (abstract lines 1-7).
Vlaminck and Cha are considered to be analogous to the claimed invention because they are all in the same field of use of amplification to detect single nucleotide variants. Therefore, 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 quantifying cell-free DNA using quantitative PCR in Vlaminck to incorporate the use of primer pairs in an amplification reaction comprising a primer pair comprising a primer with a 3’ single mismatch to a first allele and a 3’ double mismatch to a second allele and a primer pair for amplifying the second allele as taught in Cha because Cha teaches that doing so would provide a pairs of primers that achieve a sensitivity to enables measuring specific, infrequent mutations in samples.
Regarding amended claim 51, Vlaminck teaches plasma is extracted from whole blood samples to extract cell-free DNA (biological sample is blood or plasma) (pg. 7 column 2 3rd full paragraph lines 1-5).
Regarding amended claim 52, Vlaminck teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2).
Regarding amended claim 55, Vlaminck teaches that cell-free donor-derived DNA levels in the heart transplant recipients with acute rejection (transplant complication) are at levels up to 10% (in which percent concentration represents g/100mL, therefore 10g/100mL (0.1g/mL) = 0.1 = 10% and further converted from g/mL to ng/mL which is equal to 100,000,000 ng/mL) (equal to or above a threshold total cf-DNA value between 8ng/mL and 9ng/mL) (Fig.4C).
Regarding claim 56, Vlaminck teaches that this method of measuring the levels of the cell-free donor-derived DNA in heart transplant recipients provide an opportunity to diagnose and treat acute rejection through chosen threshold values to maximize sensitivity or specificity of the quantified cell-free donor-derived DNA in which therapeutic protocols include immunosuppression (anti-rejection treatment) (pg. 6 column 2 1st full paragraph lines 1-12; pg. 7 column 1 1st full paragraph lines 1-3).
Claim(s) 47 & 53 is/are rejected under 35 U.S.C. 103 as being unpatentable over Vlaminck (Vlaminck et al.; Science Translational Medicine, Vol. 6, pages 1-9, June 2014) and Cha (Cha, Zarbl, Keohavong, & Thilly; PCR Methods and Applications, Vol. 2, pages 14-20, April 1992), as applied to claims 44, 45, 49, 50-52, 55, & 56 above, and further in view of Beck (Beck et al.; Clinical Chemistry, Vol. 59, pages 1732-1741, August 2013).
The teachings of Vlaminck and Cha with respect to claim 44 & 50 are discussed above.
Regarding claim 47, Vlaminck teaches quantifying the cell-free DNA through quantitative PCR and sequencing (7 column 2 4th full paragraph lines 1-8).
Vlaminck and Cha does not teach that the quantitative PCR is real-time PCR or digital PCR.
Beck teaches a method of quantifying cell-free DNA from donor and recipient DNA from heart transplant recipients through quantitative real-time PCR using digital droplet PCR (quantitative PCR is real-time PCR or digital PCR) (abstract background lines 1-10; abstract methods lines 1-11). In addition, Beck teaches that this method of using digital droplet PCR is rapid and cost-effective method to quantify cell-free DNA in heart transplant recipients as a biomarker in early detection of rejection enabling more effective therapeutic interventions (abstract background lines 1-10; abstract conclusions lines 1-6).
Vlaminck, Cha, and Beck are considered to be analogous to the claimed invention because they are all in the same field of use of amplification. Therefore, 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 quantifying cell-free DNA using quantitative PCR in Vlaminck to incorporate the use of real-time or digital quantitative PCR as taught in Beck because Beck teaches that doing so would provide a rapid and cost-effective method to quantify cell-free DNA in heart transplant recipients as a biomarker in early detection of rejection enabling more effective therapeutic interventions.
Regarding claim 53, Vlaminck teaches quantifying the cell-free DNA through quantitative PCR and sequencing (7 column 2 4th full paragraph lines 1-8).
Vlaminck and Cha does not teach that the quantitative PCR is real-time PCR or digital PCR.
Beck teaches a method of quantifying cell-free DNA from donor and recipient DNA from heart transplant recipients through quantitative real-time PCR using digital droplet PCR (quantitative PCR is real-time PCR or digital PCR) (abstract background lines 1-10; abstract methods lines 1-11). In addition, Beck teaches that this method of using digital droplet PCR is rapid and cost-effective method to quantify cell-free DNA in heart transplant recipients as a biomarker in early detection of rejection enabling more effective therapeutic interventions (abstract background lines 1-10; abstract conclusions lines 1-6).
Vlaminck, Cha, and Beck are considered to be analogous to the claimed invention because they are all in the same field of use of amplification. Therefore, 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 quantifying cell-free DNA using quantitative PCR in Vlaminck to incorporate the use of real-time or digital quantitative PCR as taught in Beck because Beck teaches that doing so would provide a rapid and cost-effective method to quantify cell-free DNA in heart transplant recipients as a biomarker in early detection of rejection enabling more effective therapeutic interventions.
Claim(s) 50-52, 55, & 56 is/are rejected under 35 U.S.C. 103 as being unpatentable over Moreira (Moreira et al.; Clinical Chemistry, Vol. 55, pages 1958-1966, August 2009), in view of Vlaminck (Vlaminck et al.; Science Translational Medicine, Vol. 6, pages 1-9, June 2014) and Cha (Cha, Zarbl, Keohavong, & Thilly; PCR Methods and Applications, Vol. 2, pages 14-20, April 1992).
Regarding amended claim 50, Moreira teaches a method for assessing total cell-free DNA and donor derived cell free DNA as a rapid noninvasive biomarker for detection of transplant rejection through obtaining cell-free DNA from renal transplant recipients, analyzing total and donor derived cell free DNA (non-naturally occurring composition of cell-free DNA) through quantitative PCR (preparing non-naturally occurring composition of amplified DNA by performing PCR amplification on the obtained cell-free DNA), and quantifying the total cell-free DNA in the biological samples (abstract background lines 1-11; abstract methods lines 1-8; abstract results lines 1-8; pg. 1959 column 1 1st full paragraph lines 1-6; pg. 1959 column 2 1st full paragraph lines 1-40; pg. 1959-1960 paragraph bridging pg. 1959 & 1960 lines 1-8). Moreira also teaches that treatment can be administered after increase in total cell free DNA levels corresponding to rejection of the transplant (administering a treatment for a transplant complication to the transplant recipient provided the amount of cf-DNA in the biological sample is equal to or above a threshold total of cf-DNA) (pg. 1961 column 2 1st full paragraph lines 1-7) in which a cutoff total cell-free DNA concentration of 12,000 genome equivalents (GE)/mL correctly classified acute rejection episodes from non-acute rejection episodes (abstract results 1-8). Moreira also teaches that 1 GE = 6.6pg (0.0066ng), therefore a cutoff total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (pg. 1959 column 2 1st full paragraph lines 38-40).
Moreira does not teach extracting cell-free DNA from a heart transplant recipient and does not teach that the quantitative PCR comprises performing PCR with a first primer pair and a second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of SNV target but a 3’ double mismatch to a second allele of the SNV target.
Vlaminck teaches a noninvasive diagnostic method for high-throughput screening of circulating cell-free donor-derived DNA to measure acute rejection after heart transplantation through extracting cell-free DNA from whole-blood samples of the heart transplant recipient after transplant and quantifying the cell-free DNA through quantitative PCR and sequencing (abstract lines 1-11; pg. 2 column 2 3rd full paragraph lines 1-15; pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-14; pg. 7 column 1 2nd full paragraph lines 1-16; pg. 7 column 2 3rd full paragraph lines 1-5; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 4). Vlaminck also teaches that this method provides a noninvasive method that is powerful and informative in monitoring allograft health post-transplant (abstract lines 10-11).
Cha teaches a method of allele-specific PCR through the use of primers that have a single mismatch to the mutated allele at the 3’ end of the primer (first primer pair comprises a 3’ penultimate mismatch relative to a first allele of the SNV target) and a double mismatch with the wildtype allele (a double 3’ mismatch relative to a second allele of the SNV target) and primers to the wildtype allele with no mismatches (second primer pair specifically amplifies the second allele) (abstract lines 1-17; pg. 14-15 paragraph bridging pg. 14 & 15 lines 1-21; Table 1). In addition, Cha teaches that this method achieve a sensitivity that enables measuring specific, infrequent mutations in samples (abstract lines 1-7).
Moreira, Vlaminck, and Cha are considered to be analogous to the claimed invention because they are all in the same field of use of amplification. Therefore, 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 quantifying cell free DNA from a biological sample from a renal transplant recipient in Moreira to incorporate quantifying cell free DNA from a biological sample from a heart transplant recipient as taught in Vlaminck because Vlaminck teaches that doing so would provide a provides a noninvasive method that is powerful and informative in monitoring allograft health post-transplant and 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 quantifying cell-free DNA using quantitative PCR in Moreira to incorporate the use of primer pairs in an amplification reaction comprising a primer pair comprising a primer with a 3’ single mismatch to a first allele and a 3’ double mismatch to a second allele and a primer pair for amplifying the second allele as taught in Cha because Cha teaches that doing so would provide a pairs of primers that achieve a sensitivity to enables measuring specific, infrequent mutations in samples.
Regarding amended claim 51, Moreira teaches the biological sample is a blood sample (pg. 1959 column 1 1st full paragraph lines 1-6).
Regarding amended claim 52, Moreira does not teach that the PCR amplification comprises multiplex targeted PCR amplification of at least 30 SNV targets in the same reaction.
Vlaminck teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2). Vlaminck also teaches that this method provides a noninvasive method that is powerful and informative in monitoring allograft health post-transplant (abstract lines 10-11).
Moreira, Vlaminck, and Cha are considered to be analogous to the claimed invention because they are all in the same field of use of amplification. Therefore, 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 quantifying cell free DNA from a transplant recipient with quantitative PCR in Moreira to incorporate analyzing over 13,000 SNPs through PCR amplification and sequencing as taught in Vlaminck because Vlaminck teaches that doing so would provide a provides a noninvasive method that is powerful and informative in monitoring allograft health post-transplant.
Regarding amended claim 55, Moreira teaches that treatment can be administered after increase in total cell free DNA levels corresponding to rejection of the transplant (administering a treatment for a transplant complication to the transplant recipient provided the amount of cf-DNA in the biological sample is equal to or above a threshold total of cf-DNA) (pg. 1961 column 2 1st full paragraph lines 1-7) in which a cutoff total cell-free DNA concentration of 12,000 genome equivalents (GE)/mL correctly classified acute rejection episodes from non-acute rejection episodes (abstract results 1-8). Moreira also teaches that 1 GE = 6.6pg (0.0066ng), therefore a cutoff total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL (equal to or above a threshold total cf-DNA value between 8ng/mL and 9ng/mL) (pg. 1959 column 2 1st full paragraph lines 38-40).
Regarding claim 56, Moreira teaches the treatment is antirejection treatment (pg. 1963 column 1 1st full paragraph lines 2-5).
Claim(s) 53 is/are rejected under 35 U.S.C. 103 as being unpatentable over Moreira (Moreira et al.; Clinical Chemistry, Vol. 55, pages 1958-1966, August 2009), Vlaminck (Vlaminck et al.; Science Translational Medicine, Vol. 6, pages 1-9, June 2014), and Cha (Cha, Zarbl, Keohavong, & Thilly; PCR Methods and Applications, Vol. 2, pages 14-20, April 1992), as applied to claims 50-52, 55, & 56 above, and further in view of Beck (Beck et al.; Clinical Chemistry, Vol. 59, pages 1732-1741, August 2013).
The teachings of Moreira, Vlaminck, and Cha with respect to claim 50 is discussed above.
Regarding claim 53, Moreira teaches analyzing total and donor derived cell free DNA through quantitative PCR (abstract methods lines 1-8).
Moreira, Vlaminck, and Cha does not teach that the quantitative PCR is real-time PCR or digital PCR.
Beck teaches a method of quantifying cell-free DNA from donor and recipient DNA from heart transplant recipients through quantitative real-time PCR using digital droplet PCR (quantitative PCR is real-time PCR or digital PCR) (abstract background lines 1-10; abstract methods lines 1-11). In addition, Beck teaches that this method of using digital droplet PCR is rapid and cost-effective method to quantify cell-free DNA in heart transplant recipients as a biomarker in early detection of rejection enabling more effective therapeutic interventions (abstract background lines 1-10; abstract conclusions lines 1-6).
Moreira, Vlaminck, Cha, and Beck are considered to be analogous to the claimed invention because they are all in the same field of use of amplification. Therefore, 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 quantifying cell-free DNA using quantitative PCR in Moreira to incorporate the use of real-time or digital quantitative PCR as taught in Beck because Beck teaches that doing so would provide a rapid and cost-effective method to quantify cell-free DNA in heart transplant recipients as a biomarker in early detection of rejection enabling more effective therapeutic interventions.
Response to Arguments
The response traverses the rejection. The response asserts that for claims 47 & 53 Vlaminck does not disclose or suggest the independent claim limitations of preparing a non-naturally occurring composition of amplified DNA by performing target multiplex PCR amplification using a plurality of primer pairs to generate a plurality of amplicons, followed by quantitative PCR to quantify total cfDNA and that Beck does not cure these deficiencies. Further, the response asserts that, like Vlaminck, Beck quantifies donor-derived DNA as a fraction or percentage, not total cell-free DNA. Further, the response asserts that Beck does not teach or suggest at least using targeted multiplex PCR amplification with a plurality of primer pairs as required by the independent claims. Further, the response asserts that simply substituting digital PCR for Vlaminck’s sequencing-based quantification would still result in a method that quantified donor-derived DNA fraction, not total cell-free DNA as required by independent claims 44 and 50 and that Beck does not teach or suggest using digital PCR to quantify total cell-free DNA. Further, the response asserts that, with respect to claim 53, which depends from claim 50, neither Vlaminck nor Beck teaches or suggest administering treatment based on threshold total cell-free DNA values of 8-15 ng/mL. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed further above, Vlaminck teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2). Further, it is noted that the independent claims recite extracting cell-free DNA from a biological sample and further analyzing to quantify an amount of total cell free DNA in the biological sample. Further, Vlaminck teaches screening of circulating cell-free donor-derived DNA (non-naturally occurring composition of cell-free DNA) through extracting cell-free DNA from whole-blood samples of the heart transplant recipient after transplant (biological sample), quantifying the cell-free DNA through quantitative PCR and sequencing (performing PCR amplification on the cell-free DNA and preparing a non-naturally occurring composition of amplified DNA), and analyzing the cell-free donor-derived DNA levels (analyzing the non-naturally occurring composition of amplified DNA by quantitative PCR to quantify an amount of total cf-DNA in the biological sample) (abstract lines 1-11; pg. 2 column 2 3rd full paragraph lines 1-15; pg. 2-3 paragraph bridging pg. 2 & pg. 3 lines 1-14; pg. 7 column 1 2nd full paragraph lines 1-16; pg. 7 column 2 3rd full paragraph lines 1-5; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 4). Therefore, Vlaminck teaches analyzing the non-naturally occurring composition of amplified DNA by quantitative PCR to quantify an amount of total cf-DNA in the biological sample. Second, Beck teaches a method of quantifying cell-free DNA from donor and recipient DNA from heart transplant recipients through quantitative real-time PCR using digital droplet PCR (quantitative PCR is digital PCR) (abstract background lines 1-10; abstract methods lines 1-11). Therefore, Beck teaches using digital PCR to quantify total cell-free DNA. Third, Vlaminck teaches that cell-free donor-derived DNA levels in the heart transplant recipients with acute rejection (transplant complication) are at levels up to 10% (in which percent concentration represents g/100mL, therefore 10g/100mL (0.1g/mL) = 0.1 = 10% and further converted from g/mL to ng/mL which is equal to 100,000,000 ng/mL) (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (Fig.4C). Therefore, Vlaminck teaches administering treatment based on threshold equal to or above total cell-free DNA values of 8-15 ng/mL as recited in amended claim 50.
The response also asserts that claim 48 is now incorporated into claim 44 and claim 54 is now incorporated into claim 50 and that the specific primer design is not taught or suggested by the combination of cited references. Further, the response asserts that Vlaminck does not provide proper foundation for combining with Cha’s teachings as Vlaminck uses shotgun sequencing and not PCR amplification with primer pairs for cfDNA quantification and mentions quantitative PCR for library quantification and Cha teaches MAMA to detect rare somatic mutations not to quantify total nucleic acid amounts or to assess transplant complications. Further, the response asserts that neither reference teaches or suggests at least quantifying total cell-free DNA or using threshold values of 8-15 ng/mL for treating transplant complications. Further, the response asserts that one of ordinary skill in the art would have no motivation to combine Cha’s mutation detection primers with Moreira’s or Vlaminck’s methods. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed further above, Vlaminck teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through quantitative PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2). Therefore, Vlaminck teaches analyzing the non-naturally occurring composition of amplified DNA by quantitative PCR to quantify an amount of total cf-DNA in the biological sample. Further, Vlaminck and Cha are considered to be analogous to the claimed invention because they are all in the same field of use of amplification to detect single nucleotide variants. Therefore, 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 quantifying cell-free DNA using quantitative PCR in Vlaminck to incorporate the use of primer pairs in an amplification reaction comprising a primer pair comprising a primer with a 3’ single mismatch to a first allele and a 3’ double mismatch to a second allele and a primer pair for amplifying the second allele as taught in Cha because Cha teaches that doing so would provide a pairs of primers that achieve a sensitivity to enables measuring specific, infrequent mutations in samples. Further, as discussed above, Vlaminck teaches that cell-free donor-derived DNA levels in the heart transplant recipients with acute rejection (transplant complication) are at levels up to 10% (in which percent concentration represents g/100mL, therefore 10g/100mL (0.1g/mL) = 0.1 = 10% and further converted from g/mL to ng/mL which is equal to 100,000,000 ng/mL) (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (Fig.4C). Therefore, Vlaminck teaches administering treatment based on threshold equal to or above total cell-free DNA values of 8-15 ng/mL as recited.
The response also asserts the Moreira is directed to cell-free DNA as a marker of acute rejection in kidney transplant recipients, not hear transplant recipients as recited in claim 50 and that Moreira’s cutoff value of approximately 79.2 ng/mL is nearly ten times higher that the claimed threshold range od 8-15ng/mL and Moreira does not suggest its finding would apply to cardiac arrest in heart transplant recipients. Further, the response asserts that the combination of Moreira and Vlaminck does not render the claim obvious as Vlaminck does not disclose preparing a non-naturally occurring composition of amplified DNA and quantified donor-derived DNA fraction and not total cell-free DNA. Further, the response asserts that combining Moreira’s kidney transplant method with Vlaminck’s heart transplant context does not supply the claimed threshold values, which were determined through clinical studies specific to total cell-free DNA in heart transplant recipients. Further, the response asserts that the other dependent claims are also not rendered obvious by the combination of cited references as dependent claims recited PCR amplification of at least 30 SNV targets and anti-rejection or cardiac arrest treatment. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above and as, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Further, Moreira teaches that treatment can be administered after increase in total cell free DNA levels corresponding to rejection of the transplant (pg. 1961 column 2 1st full paragraph lines 1-7) in which a cutoff total cell-free DNA concentration of 12,000 genome equivalents (GE)/mL and that 1 GE = 6.6pg (0.0066ng), therefore a cutoff total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (pg. 1959 column 2 1st full paragraph lines 38-40). Further, as discussed further above, Moreira and Vlaminck are considered to be analogous to the claimed invention because they are all in the same field of detection of cell-free DNA in samples from transplant recipients. Therefore, 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 quantifying cell free DNA from a biological sample from a renal transplant recipient in Moreira to incorporate quantifying cell free DNA from a biological sample from a heart transplant recipient as taught in Vlaminck because Vlaminck teaches that doing so would provide a provides a noninvasive method that is powerful and informative in monitoring allograft health post-transplant. Further, it is noted that claim 50 as currently amened recites extracting cell-free DNA from a biological sample and does not recite that the biological sample is obtained from a specific transplant recipient. Further, as discussed further above, Vlaminck teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2) and Moreira teaches the treatment is antirejection treatment (pg. 1963 column 1 1st full paragraph lines 2-5).
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Double Patenting
Claims 44, 45, 49-51, 55, & 56 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, 6, & 9 of U.S. Patent No. 11,773,434 B2 in view of Vlaminck (Vlaminck et al.; Science Translational Medicine, Vol. 6, pages 1-9, June 2014). Although the claims at issue are not identical, they are not patentably distinct from each other because both are drawn to methods of measuring total cell free DNA in biological samples from heart transplant recipients.
It is noted that instant application claims it is a DIV of 16/623,707, now U.S. Patent No. 11,773,434, in the filing receipt dated 10/20/2023. According to MPEP 804.01(C):
The following are situations where the prohibition against nonstatutory double patenting rejections under 35 U.S.C. 121 does not apply:
…
(C) The restriction requirement was withdrawn because the requirement was written in a manner which made it clear to applicant that the requirement was made subject to the nonallowance of generic or other linking claims and such generic or linking claims are subsequently allowed.
An election of species was originally filed in the parent application 16/623,707, now U.S. Patent No. 11,773,434, which was then withdrawn in the notice of allowance office action dated 03/29/2023. Therefore, prohibition against nonstatutory double patenting rejections does not apply.
Regarding claims 44, 45, & 49, the instant application claims a method of preparing a non-naturally occurring composition of amplified DNA from a biological sample of a transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, and analyzing to quantify the amount of total cell free DNA in the biological sample and claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele (see claim 44). The instant application also claims the transplant recipient is a heart transplant recipient (see claim 49). The instant application claims the biological sample is blood, plasma, or serum (see claim 45). U.S. Patent No. 11,773,434 B2 claims a method for preparing amplified DNA from a sample from a heart transplant comprising determining whether an amount of cell free DNA is equal to or exceeds a threshold comprising extracting cell free DNA from the sample, wherein the sample is a blood, plasma, or serum sample, preparing a preparation of amplified DNA by performing PCR amplification, and analyzing the preparation of amplified DNA obtained to quantify an amount of cell free DNA and determine whether the amount of total cell fee DNA is equal or exceeds a threshold of total cell free DNA value of 8ng/mL (see claims 1 & 6). U.S. Patent No. 11,773,434 B2 also claims for SNV, performing a quantification PCR assay comprising at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 5).
U.S. Patent No. 11,773,434 B2 does not claim performing targeted multiplex PCR amplification to generate a plurality of amplicons.
Vlaminck also teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2). Vlaminck also teaches that this method is a noninvasive, powerful, and informative method for monitoring allograft health (abstract lines 10-11).
The claim would have been prima facie obvious to one of ordinary skill in the art to have modified the method of determining the amount of cell free DNA in a biological sample of a heart transplant recipient in claims 1 & 8 of U.S. Patent No. 11,773,434 B2 to incorporate analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) as taught by Vlaminck for the quantification of total cell free DNA because Vlaminck teaches that this method provides a noninvasive, powerful, and informative method for monitoring allograft health.
Regarding claims 50, 51, 55, & 56, the instant application claims a method of preparing a non-naturally occurring composition of amplified DNA from a biological sample of a transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, analyzing to quantify the amount of total cell free DNA in the biological sample, and administering a treatment provided the total amount of cell free DNA is equal to or above a threshold total cell free DNA value between 8ng/mL and 15 ng/mL or between 8 ng/ml and 9 ng/mL and claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele (see claims 50 & 55). The instant application also claims the treatment is anti-rejection treatment (see claim 56). The instant application claims the biological sample is blood, plasma, or serum (see claim 51). U.S. Patent No. 11,773,434 B2 claims a method for preparing amplified DNA from a sample from a heart transplant comprising determining whether an amount of cell free DNA is equal to or exceeds a threshold comprising extracting cell free DNA from the sample, wherein the sample is a blood, plasma, or serum sample, preparing a preparation of amplified DNA by performing PCR amplification, and analyzing the preparation of amplified DNA obtained to quantify an amount of cell free DNA, determine whether the amount of total cell fee DNA is equal or exceeds a threshold of total cell free DNA value of 8ng/mL, and administering a treatment for a transplant complication which is an anti-rejection treatment (see claims 2 & 9). U.S. Patent No. 11,773,434 B2 also claims for SNV, performing a quantification PCR assay comprising at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 5).
U.S. Patent No. 11,773,434 B2 does not claim performing targeted multiplex PCR amplification to generate a plurality of amplicons.
Vlaminck also teaches analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) (pg. 1-2 paragraph bridging pg. 1 & 2 lines 1-15; pg. 7 column 2 4th full paragraph lines 1-8; Fig. 2). Vlaminck also teaches that this method is a noninvasive, powerful, and informative method for monitoring allograft health (abstract lines 10-11).
The claim would have been prima facie obvious to one of ordinary skill in the art to have modified the method of determining the amount of cell free DNA in a biological sample of a heart transplant recipient in claims 1 & 8 of U.S. Patent No. 11,773,434 B2 to incorporate analyzing single nucleotide polymorphisms (SNPs) to discriminate between donor- and recipient-derived sequences in which over 13,000 SNPs were analyzed across all samples through PCR amplification and sequencing (comprises multiplex targeted PCR amplification of at least 30 SNV targets together in the same reaction to generate a plurality of amplicons using a plurality of primer pairs) as taught by Vlaminck for the quantification of total cell free DNA because Vlaminck teaches that this method provides a noninvasive, powerful, and informative method for monitoring allograft health.
Claims 44, 45, & 49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 15, 41, & 43 of copending Application No. 17/493,186 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both are drawn to methods of measuring total cell free DNA in biological samples from heart transplant recipients.
Regarding claim 44, the instant application claims a method of preparing a non-naturally occurring composition of amplified DNA from a biological sample of a transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, and analyzing to quantify the amount of total cell free DNA in the biological sample. Copending Application No. 17/493,186 claims a method for assaying cell free DNA from a sample from a transplant recipient comprising extracting cell free DNA from the sample, performing an amplification based quantification assay or sequencing the cell free DNA, and quantifying the total amount of cell free DNA comprising determining whether the amount of total cell free DNA is equal to or exceeds a threshold total cell free DNA value of 15 ng/mL (see claim 1). The instant application also claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele. Copending Application No. 17/493,186 claims for SNV, performing a quantification PCR assay comprising at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 15).
Regarding claim 45, the instant application claims the biological sample is blood, plasma, or serum. Copending Application No. 17/493,186 claims the sample is blood, plasma, or serum (see claim 41).
Regarding claim 49, the instant application also claims the transplant recipient is a heart transplant recipient. Copending Application No. 17/493,186 claims transplant recipient is a heart transplant recipient (see claim 43).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 50, 51, 55, & 56 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 15, 41, & 43 of copending Application No. 17/493,186 in view of Moreira (Moreira et al.; Clinical Chemistry, Vol. 55, pages 1958-1966, August 2009).
Regarding claims 50, 55, & 56, the instant application claims a method of treating a transplant complication in a heart transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, analyzing to quantify the amount of total cell free DNA in the biological sample, and administering a treatment provided the total amount of cell free DNA is equal to or above a threshold total cell free DNA value between 8ng/mL and 15 ng/mL or between 8 ng/ml and 9 ng/mL (see claims 50 & 55). The instant application also claims the treatment is anti-rejection treatment (see claim 56). The instant application claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele (see claim 50).
Copending Application No. 17/493,186 claims a method for assaying cell free DNA from a sample from a transplant recipient comprising extracting cell free DNA from the sample, performing an amplification based quantification assay or sequencing the cell free DNA, and quantifying the total amount of cell free DNA comprising determining whether the amount of total cell free DNA is equal to or exceeds a threshold total cell free DNA value of 15 ng/mL (see claim 1). Copending Application No. 17/493,186 also claims transplant recipient is a heart transplant recipient (see claim 43). Copending Application No. 17/493,186 claims for SNV, performing a quantification PCR assay comprising at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 15).
Copending Application No. 17/493,186 does not claim treating the transplant recipient provided the total amount of cell free DNA is equal to or above a threshold total cell free DNA value between 8ng/mL and 15 ng/mL or between 8 ng/ml and 9 ng/mL.
Moreira teaches a method for assessing total cell-free DNA and donor derived cell free DNA as a rapid noninvasive biomarker for detection of transplant rejection through obtaining cell-free DNA from renal transplant recipients, analyzing total and donor derived cell free DNA (non-naturally occurring composition of cell-free DNA) through quantitative PCR (preparing non-naturally occurring composition of amplified DNA by performing PCR amplification on the obtained cell-free DNA), and quantifying the total cell-free DNA in the biological samples (abstract background lines 1-11; abstract methods lines 1-8; abstract results lines 1-8; pg. 1959 column 1 1st full paragraph lines 1-6; pg. 1959 column 2 1st full paragraph lines 1-40; pg. 1959-1960 paragraph bridging pg. 1959 & 1960 lines 1-8). Moreira also teaches that treatment can be administered after increase in total cell free DNA levels corresponding to rejection of the transplant (administering a treatment for a transplant complication to the transplant recipient provided the amount of cf-DNA in the biological sample is equal to or above a threshold total of cf-DNA) (pg. 1961 column 2 1st full paragraph lines 1-7) in which a cutoff total cell-free DNA concentration of 12,000 genome equivalents (GE)/mL correctly classified acute rejection episodes from non-acute rejection episodes (abstract results 1-8). Moreira also teaches that 1 GE = 6.6pg (0.0066ng), therefore a cutoff total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (pg. 1959 column 2 1st full paragraph lines 38-40).
The claim would have been prima facie obvious to one of ordinary skill in the art to have modified the method of determining the amount of cell free DNA in a biological sample of a heart transplant recipient in claims 1 & 43 of Copending Application No. 17/493,186 to incorporate determining the total amount of cell free DNA in a heart transplant recipient with a cutoff value of total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL for treatment with anti-rejection therapy as taught by Moreira for the quantification of total cell free DNA because Moreira teaches that this method provides a rapid and noninvasive method to detect transplant rejection.
Regarding claim 51, the instant application claims the biological sample is blood, plasma, or serum. Copending Application No. 17/493,186 claims the sample is blood, plasma, or serum (see claim 41).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 44, 45, & 49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 57, & 89 of copending Application No. 16/623,719 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both are drawn to methods of measuring total cell free DNA in biological samples from heart transplant recipients.
Regarding claim 44, the instant application claims a method of preparing a non-naturally occurring composition of amplified DNA from a biological sample of a transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, and analyzing to quantify the amount of total cell free DNA in the biological sample. Copending Application No. 16/623,719 claims a method for preparing amplified cell free DNA from a sample from a transplant recipient comprising extracting cell free DNA from the sample, performing a multiplexed targeted PCR of the cell free DNA, and quantifying the total amount of cell free DNA (see claim 1). The instant application also claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele. Copending Application No. 16/623,719 claims for SNV, performing a quantification PCR assay comprising at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 57).
Regarding claim 45, the instant application claims the biological sample is blood, plasma, or serum. Copending Application No. 16/623,719 claims the sample is blood, plasma, or serum (see claim 1).
Regarding claim 49, the instant application also claims the transplant recipient is a heart transplant recipient. Copending Application No. 16/623,719 claims transplant recipient is a heart transplant recipient (see claim 89).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 50, 51, 55, & 56 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 57, 89, & 92 of copending Application No. 16/623,719 in view of Moreira (Moreira et al.; Clinical Chemistry, Vol. 55, pages 1958-1966, August 2009).
Regarding claims 50, 55, & 56, the instant application claims a method of treating a transplant complication in a heart transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, analyzing to quantify the amount of total cell free DNA in the biological sample, and administering a treatment provided the total amount of cell free DNA is equal to or above a threshold total cell free DNA value between 8ng/mL and 15 ng/mL or between 8 ng/ml and 9 ng/mL (see claims 50 & 55). The instant application also claims the treatment is anti-rejection treatment (see claim 56). The instant application claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele (see claim 50).
Copending Application No. 16/623,719 claims a method for preparing amplified cell free DNA from a sample from a transplant recipient comprising extracting cell free DNA from the sample, performing a multiplexed targeted PCR of the cell free DNA, and quantifying the total amount of cell free DNA, and further administering an anti-rejection therapy based on the determined total cell free DNA (see claim 1). Copending Application No. 16/623,719 also claims transplant recipient is a heart transplant recipient (see claim 89). Copending Application No. 16/623,719 claims for SNV, performing a quantification PCR assay comprising at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 57).
Copending Application No. 16/623,719 does not claim treating the transplant recipient provided the total amount of cell free DNA is equal to or above a threshold total cell free DNA value between 8ng/mL and 15 ng/mL or between 8 ng/ml and 9 ng/mL.
Moreira teaches a method for assessing total cell-free DNA and donor derived cell free DNA as a rapid noninvasive biomarker for detection of transplant rejection through obtaining cell-free DNA from renal transplant recipients, analyzing total and donor derived cell free DNA (non-naturally occurring composition of cell-free DNA) through quantitative PCR (preparing non-naturally occurring composition of amplified DNA by performing PCR amplification on the obtained cell-free DNA), and quantifying the total cell-free DNA in the biological samples (abstract background lines 1-11; abstract methods lines 1-8; abstract results lines 1-8; pg. 1959 column 1 1st full paragraph lines 1-6; pg. 1959 column 2 1st full paragraph lines 1-40; pg. 1959-1960 paragraph bridging pg. 1959 & 1960 lines 1-8). Moreira also teaches that treatment can be administered after increase in total cell free DNA levels corresponding to rejection of the transplant (administering a treatment for a transplant complication to the transplant recipient provided the amount of cf-DNA in the biological sample is equal to or above a threshold total of cf-DNA) (pg. 1961 column 2 1st full paragraph lines 1-7) in which a cutoff total cell-free DNA concentration of 12,000 genome equivalents (GE)/mL correctly classified acute rejection episodes from non-acute rejection episodes (abstract results 1-8). Moreira also teaches that 1 GE = 6.6pg (0.0066ng), therefore a cutoff total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL (equal to or above a threshold total cf-DNA value between 8ng/mL and 15ng/mL) (pg. 1959 column 2 1st full paragraph lines 38-40).
The claim would have been prima facie obvious to one of ordinary skill in the art to have modified the method of determining the amount of cell free DNA in a biological sample of a heart transplant recipient in claims 1 & 89 of Copending Application No. 16/623,719 to incorporate determining the total amount of cell free DNA in a heart transplant recipient with a cutoff value of total cell-free DNA concentration of 12,000 GE/mL x 0.0066ng = 79.2 ng/mL for treatment with anti-rejection therapy as taught by Moreira for the quantification of total cell free DNA because Moreira teaches that this method provides a rapid and noninvasive method to detect transplant rejection.
Regarding claim 51, the instant application claims the biological sample is blood, plasma, or serum. Copending Application No. 16/623,719 claims the sample is blood, plasma, or serum (see claim 1).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 44 & 45 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 13 of copending Application No. 16/623,725 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both are drawn to methods of measuring total cell free DNA in biological samples from transplant recipients.
Regarding claims 44 & 45, the instant application claims a method of preparing a non-naturally occurring composition of amplified DNA from a biological sample of a transplant recipient comprising extracting cell free DNA from the biological sample, preparing a non-naturally occurring composition of amplified DNA by performing PCR amplification on the cell free DNA, and analyzing to quantify the amount of total cell free DNA in the biological sample. The instant application also claims the biological sample is blood, plasma, or serum (see claim 45). The instant application also claims that the PCR amplification comprises multiplex target PCR amplification of at least 30 SNV targets together in the same reaction (see claim 44). The instant application claims the quantitative PCR comprises for each SNV target, performing PCR using a first and second primer pair, wherein the first primer pair comprises a 3’ penultimate mismatch in a primer relative to a first allele of the SNV target but a 3’ double mismatch relative to a second allele, and wherein the second primer pair specifically amplifies the second allele (see claim 44). Copending Application No. 16/623,725 claims a method for preparing amplified cell free DNA from a sample from a transplant recipient comprising extracting cell free DNA from the sample, wherein the sample id blood, plasma, or serum sample, performing a multiplexed targeted PCR of the cell free DNA to amplify at least 50 SNV targets in the same reaction, performing quantitative PCR to quantify the total amount of cell free DNA, performing quantitative PCR using at least two primer pairs, wherein one primer pair comprises a 3’ penultimate mismatch in a primer relative to a one allele of the SNV target but a 3’ double mismatch relative to a another allele, and wherein the another primer pair specifically amplifies the other allele (see claim 13).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
The response traverses the rejection. The response asserts that the pending application is a divisional of Application No. 16/623,707, now U.S. Patent No. 11,773,434 and as a divisional application, the pending claims are entitled to the safe harbor protections of 35 U.S.C. 121. Further, the response asserts that the pending claims recite specific elements including performing multiplex PCR amplification to generate a plurality of amplicons and this specific claim language is not recited in the claims of the ‘434 patent. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed previously and above, It is noted that instant application claims it is a DIV of 16/623,707, now U.S. Patent No. 11,773,434, in the filing receipt dated 10/20/2023. According to MPEP 804.01(C):
The following are situations where the prohibition against nonstatutory double patenting rejections under 35 U.S.C. 121 does not apply:
…
(C) The restriction requirement was withdrawn because the requirement was written in a manner which made it clear to applicant that the requirement was made subject to the nonallowance of generic or other linking claims and such generic or linking claims are subsequently allowed.
An election of species was originally filed in the parent application 16/623,707, now U.S. Patent No. 11,773,434, which was then withdrawn in the notice of allowance office action dated 03/29/2023. Therefore, prohibition against nonstatutory double patenting rejections does not apply. Second, as necessitated by amendment, Claims 44, 45, 49-51, 55, & 56 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, 6, & 9 of U.S. Patent No. 11,773,434 B2 in view of Vlaminck (Vlaminck et al.; Science Translational Medicine, Vol. 6, pages 1-9, June 2014), as discussed further above.
The response also traverses the remaining provisional nonstatutory double patenting rejections and requests that they be held in abeyance as applicant will address the rejections, or take appropriate action, as deemed necessary, upon the indication that the present application is found otherwise to be in conditions of allowance.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 44, 45, 47, 49-53, 55, & 56 are rejected.
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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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/ Primary Examiner, Art Unit 1682
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