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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 5/28/2026 has been entered.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 1-3, 6-7, 10-11, 13, 20-21, 24-25, 30, 33, 36, 45-48, and 64 are pending and are examined on the merits herein.
Response to Applicant’s Amendments and Arguments
Claims 1-2, 6-7, 10-11, 13, 20-21, 24-25, 30, 33, 36, and 45-47 were rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), and in view of Christians et al. (US 2017/0275691 A1).
Claim 3 was rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), in view of Christians et al. (US 2017/0275691 A1), and further in view of Favalli (WO 2019/149673 A1).
Claim 48 was rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), in view of Christians et al. (US 2017/0275691 A1), and further in view of Knight et al. (Transplantation, 2019).
Claim 64 was rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), and further in view of Favalli (WO 2019/149673 A1).
Regarding the 35 USC 103 Rejections, Applicant argues that the references cited in the Final Rejection mailed 1/28/2026 do not teach or suggest quantifying the total amount of sequence reads derived from Tracer DNA, and specifically, that Zhang’s Figures 8-9 and Examples 8 and 11 do not read on this limitation (Remarks, pages 10-12). Regarding the construction of the Tracer DNA, Applicant argues that the claimed limitation “the pair of primer binding sites in the target sequence is capable of binding to one of the 100 or more different primer pairs,” meaning that at least one of the primers used for amplifying the target loci must also be capable of binding to the Tracer DNA, is not taught by the combination of references. Furthermore, altering the teachings of Christians to arrive at this limitation would allegedly not be ordinary creativity under KSR (Remarks, pages 12-13).
Additionally, regarding claim 64, Applicant similarly argues that neither Zhang nor Favalli teach quantifying an absolute amount of donor cfDNA and (Remarks, pages 14-15).
Regarding the teachings of Zhang, the Examiner agrees that Figure 8 is focused on the number of sequence reads present, and Figure 9 is focused on finding a foreign fraction, which involves using the total number of molecules in a sample, which does not directly relate to absolute quantification. However, in both cases, if the total number of sequence reads is known, and the number of foreign sequence reads is also known, then the number of sample cfDNA sequence reads would also be known. Example 8 (and the corresponding Table 2) of the reference shows absolute quantification of two genomic DNA samples via SNP profiling (paras. 119-120). In Example 11, two spike-in sequences (in known concentrations) were used to validate the ability of the methods of Zhang to quantify foreign DNA. These are used, along with other teachings provided by the reference, to arrive at the claimed quantification. If a spike-in, with a known concentration, is correlated with a particular amount of sequence reads in a final volume of solution with a cfDNA sample and the spike-ins, then the ordinary artisan would be capable of using this information, along with the total number of sequence reads (which would be available through sequencing methods), to perform basic analysis methods to determine the number of sequence reads corresponding to the cfDNA, and to then correlate the number of sequence reads of the sample cfDNA with a concentration as well. Such as assertion is also supported by the spike-ins of Christians, which are used for quantification purposes (paras. 92, 95, 97, and 410). This reads on the quantification of instant claim 1. In instant claim 2, similar calculations could be made to determine the amount of cfDNA in a sample, and as Zhang clearly teaches that donor and recipient derived DNA can be distinguished from one another during sequencing analyses (Figures 8 and 9), such distinctions could be made to then determine the amounts of donor and recipient DNA within the calculated amount of sample cfDNA. It is noted that this rationale is also relevant to the arguments against claim 64 regarding quantification.
Regarding the structure of the Tracer DNA, the Examiner notes the following teachings and rationale from Babiarz that have not previously been made of record. Babiarz teaches that the amplification used in their methods can be used for absolute quantification of spike calibrators (para. 399). Elsewhere throughout the reference, the use of genetic standards is taught, where said standards are calibrated to a reference genome and are provided in a known amount, where these standards also involve the use of “a first universal priming site, a second universal priming site, a first target specific priming site, a second target specific priming site, and a marker sequence located between the first and second target specific priming sites, wherein the first target specific site and the second target specific priming site are located between the first and second universal priming sites,” where calibration can involve using any of the primer libraries of the invention (para. 67), and wherein the calibration can occur during the method of the invention (para. 69). In employing these standards, standards for particular loci are designed so that they can amplify with the same efficiency as their corresponding loci (para. 505). In para. 510, it states, “The standard sequences may be selected to be very similar in nucleotide base sequence to the amplified regions of interest; preferably the standard sequence has the exact same primer-binding sites as the analyzed genomic region, i.e., the “target sequence.”” By using the same primer binding sites for the target and the standard, Babiarz teaches that this would, “minimize any amplification discrimination between the gene of interest and the standard sequence corresponding to the gene of interest,” (para. 514). These teachings are used in new grounds of rejection below regarding the instant claims, where Babiarz is used to teach the claimed structure of the Tracer DNA sequences. Therefore, Applicant’s arguments against Christians for this point are moot.
Thus, overall, Applicant’s arguments are not considered persuasive to obviate the use of the references cited in the Final Rejection. However, as noted above, teachings of Babiarz that were not previously used in the obviousness rejections have been incorporated into the rejections herein. These teachings also lead to rationale not previously employed by the Examiner, and so although the claims remain rejected over Zhang, in view of Babiarz, and in view of Christians (and additional references were relevant), these are considered new grounds of rejection, and all previously set forth 35 USC 103 Rejections have been withdrawn.
Claim Interpretation
The phrase “non-naturally occurring composition” is not specifically defined in the instant specification, and in fact does not appear in the instant specification. However, the claimed compositions would inherently be non-naturally occurring, as they involve amplification methods and primer sequences that would not be found naturally.
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2, 6-7, 10-11, 13, 20-21, 24-25, 30, 33, 36, and 45-47 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), and in view of Christians et al. (US 2017/0275691 A1).
Zhang teaches methods of quantifying foreign cell-free DNA in blood samples (Abstract). Para. 21 describes a method of monitoring organ rejection via extraction of cell-free DNA and genomic DNA from an organ transplant recipient, amplifying short fragments of cell-free DNA, obtaining sequence reads for at least 500 SNPs, and quantifying donor versus recipient cell-free DNA. The DNA may be extracted from whole blood and isolated from plasma (paras. 13 and 22; instant claim 46). The nucleic acids used in the invention can be from a human sample (paras. 54, 61, 73; instant claim 36). Zhang teaches methods of sequence analysis when donor genotype is both known and unknown (paras. 23-24), and shows workflows where donor genotype is explicitly not required (para. 42 and Figure 9; instant claim 45). These methods rely on quantifying total numbers of SNPs (i.e. total cell-free DNA) before determining which portions of sequence reads are from donor-derived cfDNA (Figures 8 and 9). Zhang describes methods for selectively amplifying cfDNA in a sample with genomic DNA (para. 36 and Figures 3A-3C, which involve incorporating adapters into the ends of the cfDNA). 500-1,000,000 SNPs may be targeted (para. 45).
Zhang also teaches the use of spike-in DNA to detect donor-derived cfDNA in a sample, where a known amount of foreign DNA is added to an existing DNA sample (paras. 119-120 and 130, Examples 8 and 11). By providing a known value of introduced foreign DNA and then later detecting that DNA, this can be used to determine the amount of foreign (i.e. donor) DNA in a sample (Figure 10). Zhang teaches that this information can be used to monitor the occurrence of transplant rejection (para. 130). It is noted that Example 11 in particular utilizes the methods of Example 10, which are shown in Figure 9 and clearly lay out a method for determining the amount of foreign DNA present in a sample. Table 2 also explicitly shows sequencing results when using spike-in sequences.
As noted above in the “Response to Applicant’s Arguments section,” Figure 8 of Zhang is focused on the number of sequence reads present, and Figure 9 is focused on finding a foreign fraction, which involves using the total number of molecules in a sample, which does not directly relate to absolute quantification. However, in both cases, if the total number of sequence reads is known, and the number of foreign sequence reads is also known, then the number of sample cfDNA sequences would also be known. Example 8 (and the corresponding Table 2) of the reference shows absolute quantification of two genomic DNA samples via SNP profiling (paras. 119-120). In Example 11, two spike-in sequences (in known concentrations) were used to validate the ability of the methods of Zhang to quantify foreign DNA. If a spike-in, with a known concentration, is correlated with a particular amount of sequence reads in a final volume of solution with a cfDNA sample and the spike-ins, then the ordinary artisan would be capable of using this information, along with the total number of sequence reads (which would be available through sequencing methods), to perform basic analysis methods to determine the number of sequence reads corresponding to the cfDNA, and to then correlate the number of sequence reads of the sample cfDNA with a concentration as well. This reads on the quantification of instant claim 1 and instant claim 20. In instant claim 2, similar calculations could be made to determine the amount of cfDNA in a sample, and as Zhang clearly teaches that donor and recipient derived DNA can be distinguished from one another during sequencing analyses (Figures 8 and 9), such distinctions could be made to then determine the amounts of donor and recipient DNA within the calculated amount of sample cfDNA. Thus, Zhang shows that spike-in sequences can be used to quantify foreign DNA in a sample, with particular uses for quantifying donor-derived cfDNA and making transplant rejection determinations. The ordinary artisan would thus be motivated to include these spike-in methods in the methods of Zhang described above, to aid in quantifying cfDNA and to monitor organ transplant patients, as methods involving the use of a standard (such as a spike-in sequence) can allow for more accurate quantification and better comparison of cfDNA values in a patient over time and/or between different patients, allowing analysis results to be more useful and widely-applicable.
However, Zhang does not teach that the amplification used in their method relies on the use of 100 or more different primer pairs in a single reaction volume – Zhang appears to rely on the use of universal primers that hybridize to ligated adaptors (e.g. paras. 6, 9, and 11). Additionally, Zhang does not teach that their spike-in sequences contain a barcode positioned between primer binding sites.
Babiarz teaches methods for simultaneously amplifying multiple nucleic acids of interest in a single reaction volume (Abstract). These methods can involve a first non-specific amplification step, followed by specific and simultaneous amplification of at least 1,000 non-identical loci in a reaction mixture (where up to 100,000 target loci can be amplified), and at least 1,000 primer pairs (and up to 100,000 primer pairs) can be used (paras. 12-13). The target DNA can come from DNA of a mixed origin (such as DNA resulting from transplantation; para. 395), and Babiarz specifically teaches analyzing cell-free DNA from transplant recipients, where some of the cfDNA is from donors, and the method can be used to, “prognose, diagnose, detect, or monitor a transplant status or outcome, such as a transplant, tolerance, non-rejection based allograft injury, transplant function, transplant survival, chronic transplant injury, or tittering of pharmacological immunosuppression,” (para. 408). The reference teaches that performing a universal amplification step before targeted amplification can have advantages, such as removing the risk of bottlenecking and reducing allelic bias (para. 454). A universal amplification step can also be used to increase overall sample quantity, which can aid in minimizing bias (para. 368). Babiarz also states, “Greater multiplexing allows more alleles to be targeted, giving more accurate results. Better uniformity results in more of the targeted alleles being measured, giving more accurate results. Lower rates of allelic bias result in lower rates of miscalls, giving more accurate results. More accurate results result in an improvement in clinical outcomes, and better medical care,” (para. 475).”
Additionally, Babiarz teaches that the amplification used in their methods can be used for absolute quantification of spike calibrators (para. 399). Elsewhere throughout the reference, the use of genetic standards is taught, where said standards are calibrated to a reference genome and are provided in a known amount, where these standards also involve the use of “a first universal priming site, a second universal priming site, a first target specific priming site, a second target specific priming site, and a marker sequence located between the first and second target specific priming sites, wherein the first target specific site and the second target specific priming site are located between the first and second universal priming sites,” where calibration can involve using any of the primer libraries of the invention (para. 67), and wherein the calibration can occur during the method of the invention (para. 69). In employing these standards, standards for particular loci are designed so that they can amplify with the same efficiency as their corresponding loci (para. 505). In para. 510, it states, “The standard sequences may be selected to be very similar in nucleotide base sequence to the amplified regions of interest; preferably the standard sequence has the exact same primer-binding sites as the analyzed genomic region, i.e., the “target sequence.”” By using the same primer binding sites for the target and the standard, Babiarz teaches that this would, “minimize any amplification discrimination between the gene of interest and the standard sequence corresponding to the gene of interest,” (para. 514). The reference also teaches that their methods can be used for absolute quantification of DNA from the donor of a DNA transplant (para. 408), and para. 505 notes that known quantities of standards can be absolute (para. 505). Para. 507 states, “Standard sequences can be added during the process of library formation (prior to amplification) in known quantities (relative or absolute) so as to provide a standard metric for greater accuracy in determining the amount of target sequence of interest in the sample of analysis.”
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to combine the methods of Zhang and Babiarz. Firstly, Zhang teaches the targeting of at least 500 SNPs via universal amplification and sequencing methods, and Babiarz teaches that universal amplification can be followed by specific amplification involving primer pairs that target particular loci. Babiarz teaches a multitude of advantages to using this method that would motivate the ordinary, including reduced bias and increased accuracy. Zhang and Babiarz also both teach that their methods can analyze cfDNA in the context of organ transplants and transplant rejections. There would be a reasonable expectation of success because Babiarz shows that such multiplexed single reaction amplification can successfully be performed (e.g. para. 835 and Figure 15; instant claim 30), and that these methods can work with standard sequences (e.g. spike-in sequences).
Additionally, it would be prima facie obvious that if the general amplification method of Babiarz, with its universal step followed its target-specific step, were used in Zhang in view of Babiarz, that the spike-in sequences of Zhang could be structurally modeled after the standards of Babiarz, which were designed to undergo such amplification reactions. This would result in spike-ins that had two universal priming sites and two target-specific binding sites located within the universal primer binding sites, where the primer binding sites of the spike-ins are the same as those of the target, and the spike-in sequences are nearly identical to those of the target sequences. Babiarz teaches that such a structure would ensure that standards and targets are amplified with the same efficiency, which would produce more accurate results, motivating the ordinary artisan. Additionally, both Zhang and Babiarz encompass absolute quantification and providing known amounts of spike-in/target sequences, providing further evidence that their combination would read on the quantification of the instant claims. There would be a reasonable expectation of success in employing these design methods because they are already shown to be compatible with the amplification methods of Babiarz.
However, Babiarz does not teach spike-in sequences that contain a barcode positioned between primer binding sites. The reference teaches that primers may have molecular barcodes (paras. 388 and 407), which would result in the standards of the reference also containing molecular barcodes, but is not specific about where such barcodes would be relative to other features of the primers/standards.
Christians teaches methods of making and using synthetic nucleic acids (Abstract). The synthetic nucleic acids may be spike-ins, where they can be used with targets for eventual sequencing (paras. 3-4 and 7), and they can be added at the start of sample processing (para. 10). The spike-ins may have an identifying tag sequence (para. 8), and can be generated via the use of PCR (paras. 144 and 147). Thus, the spike-in sequences would have primer binding sites on either end. The spike-in sequences can also have adapters (para. 143) and these adapters can be primer binding sites (para. 112). Sets of spike-ins may be used, where the sets may have different species with different lengths, concentrations, and/or sequences (paras. 132-133). These spike-ins can be used for sample tracking, monitoring cross-contamination, tracking reagents, and normalization, among other uses (para. 132). The tags of Christians can be useful for analyzing sequence reads (para. 216), and these tags may be “embedded within each spiked molecule,” (para. 412). The spike-in sequences generally may have specifically designed sequences (paras. 92-93).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the spike-in teachings of Christians to inform those of Zhang in view of Babiarz. As Christians does not require a specific location for the tag sequences, and notes they may be embedded within sequences, it would be obvious to include the tag in the middle of the spike-in sequences. This is because these tags are useful for identifying sequence reads, and by including them away from the ends of the spike-in sequences, it can ensure that these tag sequences remain intact and are not lost or degraded through the amplification and sequencing processes. Specifically, as the spike-in sequences of Zhang in view of Babiarz have two sets of primer binding sites (the universal and the target-specific sites), including the tag within both of these sets would ensure that both amplification reactions work as intended. In combining Christians with Zhang in view of Babiarz, there would be a reasonable expectation of success as Christians processes spike-ins in a method similar to that of Zhang in view of Babiarz successfully, and Zhang is not specific about required or prohibited spike-in structure (instant claims 1-2).
Thus, claims 1-2, 20, 30, 36, and 45-46 are prima facie obvious over Zhang, in view of Babiarz, and in view of Christians.
Regarding claim 6, Zhang teaches that “if the fraction of the short fragments of cell-free DNA that correspond to the DNA of the organ transplant donor is above a normal range or increases over time, then the organ transplant recipient is considered to be rejecting the transplanted organ,” (para. 27). Para. 97 notes that, “When the organ from the donor is rejected and attacked by the immune system, the concentration of cfDNA derived from the dying rejected organ’s cells will significantly increase.” Figure 11 also details the foreign molecule percentage in healthy individuals and non-rejection organ recipients (para. 44), which would require a determination of total amount of cell-free DNA present (see Figures 8-9 for details on how donor fraction is determined). This information would render obvious the limitation of instant claim 6. Specifically, Zhang teaches determining the level of cell-free DNA in a sample, as noted above in the rejection of claim 2. Zhang also notes that in cases of transplant rejection, donor cell-free DNA goes up, and thus, the total cell-free DNA level in a sample would also go up. Zhang also notes the normal range of donor cell-free DNA present in transplant recipients, which would require a determination of the normal range of total cell-free DNA present in transplant recipients. This information could be combined to determine a normal total cell-free DNA range, and then as samples are evaluated, numbers greater than this range could be used to further examine the associated subject for potential transplant rejection.
Regarding claim 7, Zhang teaches that their spike-in sequences are added to pure DNA samples (paras. 119 and 130). Thus, it would be prima facie obvious to add the spike-ins to the composition comprising the isolated cfDNA in Zhang, in view of Babiarz, and in view of Christians above to ensure the spike-in sequences were subjected to the same processing as the cfDNA.
Regarding claim 10, Zhang teaches the use of universal adaptors attached to cfDNA sequences (see Figures 3A-C, as noted above). As these are added before amplification occurs, and as noted in the rejection of claims 1 and 7 above, the spike-in sequences are added before sample analysis begins, the spike-ins would be added before the adaptors are ligated.
Regarding claim 11, Babiarz teaches that the number of sequences standards used can correspond to the number of target sequences to be analyzed (paras. 66-69), and teaches a plurality of standards throughout the invention (paras. 505 and 507-510). As Zhang teaches the analysis of at least 500 SNPs (para. 21), there would be more than one target sequence analyzed in the method of Zhang, in view of Babiarz, and in view of Christians, and therefore would be more than one spike-in/sequence standard used. It would be prima facie obvious to introduce each spike-in/sequence standard at the same time in the overall method, so that they may all be amplified in the same manner and produce similar numbers of products, and therefore can be analyzed in downstream methods similarly. Furthermore, it would be prima facie obvious that the spike-in/sequence standards would all be designed the same way, with the universal and target primer sequences as described above in the rejection of claim 1, so that all the spike-in/sequence standards would be amplified with similar efficiency compared to their respective target sequences.
Regarding claim 13, the spike-ins used by Zhang, in view of Babiarz, and in view of Christians are based on the different cfDNA target sequences provided, and so would naturally have different sequences.
Regarding claims 25 and 33, Zhang teaches that their spike-ins are genomic DNA (e.g. para. 119) and thus may be double-stranded, and teaches that cfDNA is usually about 160 nucleotides in length (para. 99). After manipulation of cfDNA in their methods, the lengths of the fragments are about 300bp (para. 103). Such final lengths are compatible with the use of the primers of Babiarz, as this reference teaches that primer sequences can be from 15-100 nucleotides (e.g. para. 15). As the spike-in sequences of Zhang, in view of Babiarz, and in view of Christians are designed to correlate almost perfectly with the target sequences, it would be prima facie obvious that said spike-ins would thus also be around 160 nucleotides, in order to retain the amplification efficiency benefits discussed by Babiarz above with regard to similarity between the spike-in and target sequences.
Furthermore, regarding claims 21 and 24, in the method of Zhang, in view of Babiarz, and in view of Christians described above in the rejection of claim 25, genomic DNA spike-ins are used. As the cfDNA used is from a patient sample, and would thus contain genomic DNA sequences from the patient, and the spike-in sequences are designed to be nearly identical to target sequences, it would be prima facie obvious to use fragmented genomic DNA sequences (that are present in the cfDNA) from the patient as the core of the spike-in sequences, where these sequences would be surrounded by primer binding sites and would contain a barcode. These genomic sequences are already provided by the sample, making them easy to obtain, and would significantly cut down on the time required to design the spike-in sequences, as they could simply be modified by the ordinary artisan as needed to produce the spike-in structure described above (instant claim 24). Furthermore, as noted above, the spike-in sequences may be double-stranded, and so each portion of the sequence would have a corresponding complement/reverse complement. Thus, it would be prima facie obvious that the spike-ins in Zhang, in view of Babiarz, and in view of Christians would have regions that are reverse complementary to a portion of genomic DNA, from which the spike-in is made, on the second strand of the double-stranded spike-in.
Regarding claim 47, Zhang teaches noting the fraction of donor cfDNA over time to determine if an organ transplant recipient is rejecting the transplanted organ (para. 27). To determine if the level of donor cfDNA is increasing over time, it would be obvious to the ordinary artisan that the level of donor cfDNA would have to be measured at multiple time points, and thus, the method described above in the rejection of claim 2 would be repeated at each time point.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), in view of Christians et al. (US 2017/0275691 A1), and further in view of Favalli (WO 2019/149673 A1).
Regarding claim 3, Zhang, in view of Babiarz, and in view of Christians teaches the method of claim 2, as described above.
However, neither Zhang, nor Babiarz, nor Christians teach the specific use of thresholds in relation to transplant rejection.
Favalli teaches the detection of donor cfDNA in organ transplant recipients to provide an early indication of transplant rejection (Abstract). The reference teaches that during rejection episodes, circulating donor DNA may increase from 1%-5% in organ recipients, and an increase of over 5% can indicate the beginning of a rejection (page 12, para. 1). Favalli teaches calculations for determining the amount of donor cfDNA in a sample (page 15). They teach that an increase in the level of cfDNA between 5-15% is indicative of the probable presence of rejection, and an increase of 10-25% can be indicative of clinically significant rejection (page 18, para. 4).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Favalli with the methods of Zhang, in view of Babiarz, and in view of Christians to arrive at the invention of claim 3. Specifically, the thresholds established by Favalli could be used to determine if a patient is at risk of transplant rejection (1-5%) or is likely experiencing transplant rejection (>5%). Zhang teaches comparing donor cfDNA levels within a patient over time (para. 27), but does not note a specific threshold. By providing a specific threshold, risk of rejection can be measured in a standardized way across multiple patients. A specific threshold also allows for invasive interventions to only be performed if they are necessary, and not simply because the amount of donor cfDNA in a sample increased marginally between testing windows. Because Zhang teaches quantification of total cfDNA, donor cfDNA is a function of total cfDNA, and the threshold taught by Favalli is a function of the amount of cfDNA, these combined teachings are considered to meet the teachings of instant claim 3.
Thus, claim 3 is rejected as prima facie obvious over Zhang, in view of Babiarz, in view of Christians, and further in view of Favalli.
Claim 48 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), in view of Christians et al. (US 2017/0275691 A1), and further in view of Knight et al. (Transplantation, 2019).
For this claim, it is noted that while at least two donors must be provided, there is no requirement that in the quantification of donor-derived cfDNA, that the contributions of the first and second donors be separately quantified.
Zhang, in view of Babiarz, and in view of Christians teaches the method of claim 2, as described above. However, neither reference teaches the use of multiple organ donors.
Knight teaches the measurement of donor cfDNA as a biomarker in solid organ transplantation (Abstract). The reference teaches the evaluation of data from various sources, and several studies included data from multiorgan transplants (Abstract). Table 1 shows the successful detection of cfDNA in multiple multiorgan samples from the plasma of patients.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the information provided by Knight to evaluate multiorgan transplant recipients with the method of Zhang, in view of Babiarz, and in view of Christians. The presence of a second transplanted organ provides additional risk of transplant rejection, and so these patients require intensive monitoring. By providing a non-invasive monitoring method, this would improve patient comfort while still closely monitoring donor cfDNA levels in the blood, and would allow for quick action upon a noted increase in these levels.
Thus, claim 48 is rejected over Zhang, in view of Babiarz, in view of Christians, and further in view of Knight.
Claim 64 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (WO 2020/118046 A1), in view of Babiarz et al. (US 2016/0369333 A1), and further in view of Favalli (WO 2019/149673 A1).
Regarding claim 64, it is noted that the limitations of the claim are mostly met by the teachings of Zhang in view of Babiarz described above in the rejection of claim 2 (claim 64 does not require the Tracer DNA of claim 2, and so the teachings of Christians are not required, see paras. 19-26 of the rejection above for the specific teachings of Zhang in view of Babiarz), in combination with the following: these references also teach analyzing over 500 loci (500 SNPs are noted in Zhang, para. 21 for example, and Babiarz teaches at least 1,000 loci in paras. 12-13) and the use of a blood sample (Zhang para. 22). Zhang also teaches quantifying donor-derived cfDNA (para. 21), and teaches this quantification by finding the percentage of donor cfDNA over the total amount of cfDNA (e.g. Figures 8-9).
However, neither Zhang nor Babiarz teach the specific use of thresholds in relation to transplant rejection.
Favalli teaches the detection of donor cfDNA in organ transplant recipients to provide an early indication of transplant rejection (Abstract). The reference teaches that during rejection episodes, circulating donor DNA may increase from 1%-5% in organ recipients, and an increase of over 5% can indicate the beginning of a rejection (page 12, para. 1). Favalli teaches calculations for determining the amount of donor cfDNA in a sample (page 15). They teach that an increase in the level of cfDNA between 5-15% is indicative of the probable presence of rejection, and an increase of 10-25% can be indicative of clinically significant rejection (page 18, para. 4).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Favalli with the methods of Zhang in view of Babiarz to arrive at the invention of claim 64. Specifically, the thresholds established by Favalli could be used to determine if a patient is at risk of transplant rejection (1-5%) or is likely experiencing transplant rejection (>5%). Zhang teaches comparing donor cfDNA levels within a patient over time (para. 27), but does not note a specific threshold. By providing a specific threshold, risk of rejection can be measured in a standardized way across multiple patients. A specific threshold also allows for invasive interventions to only be performed if they are necessary, and not simply because the amount of donor cfDNA in a sample increased marginally between testing windows. Because Zhang teaches quantification of total cfDNA, donor cfDNA is a function of total cfDNA, and the threshold taught by Favalli is a function of the amount of cfDNA, these combined teachings are considered to meet the teachings of instant claim 64.
Thus, claim 64 is rejected as prima facie obvious over Zhang, in view of Babiarz, and further in view of Favalli.
Conclusion
No claims are currently allowable.
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/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
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