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 .
Response to Amendment
The amendment filed 26 January 2026 is acknowledged. The amendment focused the limitations of claim 1 to under-represented structural variants and incorporated the limitations of claim 17 into claim 11.
Regarding the Office Action mailed 12 December 2025:
The rejections of claim 17 are withdrawn as the claim has been canceled.
The rejections of claims 1-16 and 18-24 under 35 USC § 103 are maintained and reiterated below; applicant’s remarks will be addressed following the rejections.
The nonstatutory double patenting rejections of claims 1-16 and 18-24 over claims 1-13 of U.S. Patent No. 11,066,707 in view of Coccaro are maintained.
The provisional nonstatutory double patenting rejections of claims 11-16 and 18-24 over claims 40-46 and 51-53 of copending Application No. 17/361,829 are maintained.
The provisional nonstatutory double patenting rejections of claims 1-16 and 18-24 over claims 6-22 of copending Application No. 18/204,703 are maintained.
Claim Rejections - 35 USC § 103
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.
Claims 1-11, 15-17, and 19-24 are rejected under 35 U.S.C. 103 as being unpatentable over Jackson [Jackson et al., Journal of Molecular Diagnostics, 2016, Vol. 18(2), 235-43] in view of Coccaro [Coccaro et al., International Journal of Molecular Science, 2020, Vol. 21(9), 3141].
Regarding claim 1, Jackson teaches a method for detecting tumor-specific mutations present in a sample in low abundance relative to wild-type circulating, cell-free DNA (ccfDNA), which had previously made their detection technically challenging [abstract]. This method entails performing pre-amplification on a sample [p236, col2, para2], followed by analysis with droplet PCR (dPCR), ultimately resulting in the detection of cancer-relevant mutations [abstract].
However, Jackson does not teach first identifying sequences under-represented in a sample upon which to perform their 2-step amplification process.
Coccaro, however, reports on one study in which sequences were first identified using either nanopore sequencing or fluorescence in situ hybridization followed by Sanger sequencing, and were then assessed using ddPCR as a means for “personalized monitoring” of a patient [Coccaro, pg7, para4].
Therefore, it would have been obvious to one of ordinary skill in the art prior to the effective filling date of the claimed invention to first identify sequences of interest (as demonstrated in Coccaro) before performing the method of Jackson in order to target tumor-specific sequences relevant for cancer detection and progression monitoring.
The use of a known technique to improve similar devices (methods or products) in the same way is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, C.).
Regarding claim 2, Jackson demonstrates the use of PCR in the pre-amplification step [p236, col2, para2], which is known in the art as producing exponential amplification of a target.
Regarding claims 3 and 22, Coccaro reports on multiple studies which show that gene rearrangements can be used as molecular markers for cancer detection and monitoring, even in instances where the disease load is very low [Coccaro, pg7 para4, pg8 para1, pg11 para3]. Jackson further states that their method is capable of detecting base substitutions, insertions, deletions, and chromosomal duplications [Jackson, p256, col1, para1].
Regarding claim 4, Coccaro teaches that the detection of tumor-relevant targets can be used to monitor minimal residual disease (Coccaro, pg5-8, section 3).
Regarding claims 5, 10, and 23, Jackson obtained tissue and blood samples from cancer patients [p236, col2, para3] and the pre-amplification step was performed on serum-derived ccfDNA [p237, col2, para2].
Regarding claims 6 and 7, Jackson and Coccaro teach the limitations of claims 1 and 3 as previously described. However, neither specifically state that the results of the described methods and assays could be used to report on the structural rearrangements and genomic mutations present or on the presence of a tumor in a subject.
However, Jackson discusses the use of their method to detect cancer relevant markers [Jackson, abstract]. Coccaro further states that the methods in their report can be used for a variety of applications including mutation detection, MRD monitoring, transplantation assessment, discrimination of transcript variants, etc. (Coccaro, pg3, Fig1).
Therefore, it would have been obvious to one of ordinary skill in the art prior to the effective filling date of the claimed invention to report the presence of a tumor/structural rearrangements/genomic mutations based upon positive results obtained from Jackson’s method as modified by Coccaro in order to aid in clinical diagnoses and decisions regarding treatment and prognosis.
The combination of familiar elements is likely to be obvious when it does no more than yield predictable results. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, A.).
Regarding claim 8, Jackson and Coccaro teach the limitations of claims 1 and 3 (as discussed previously), but fail to teach selecting a target that would be likely to persist in a tumor.
However, the ultimate goal of both is to address the detection and monitor the progression of cancer [Jackson, p236, col1, para1; Coccaro, abstract]. Furthermore, as previously described, Coccaro describes methods for selecting targets relevant to MRD monitoring.
Therefore, it would be obvious to one of ordinary skill in the art prior to the effective filling date, motivated to monitor cancer progression, to choose a persistent marker in order to accurately access the progression of a tumor before and after treatment, as non-persistent markers would lead to false-negatives.
The combination of familiar elements is likely to be obvious when it does no more than yield predictable results. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, A.).
Regarding claim 9, Jackson teaches partitioning the pre-amplified sample into droplets, and performing subsequent PCR and signal detection in these droplets [p237, col2, para4 – p238, col 1, para-2].
Regarding claim 11, Jackson teaches a method for detecting tumor-specific mutations in a sample [Jackson, abstract] by performing pre-amplification of a target region [p236, col2, para2], followed by analysis with droplet PCR (dPCR), ultimately resulting in the detection of cancer-relevant mutations [abstract]. Furthermore, Coccaro shows that these cancer-relevant mutations can include genomic rearrangements [Coccaro, pg7, para4].
Regarding claims 1, 15-16, 19-21, and 24, Jackson teaches diluting the pre-amplified reaction mixture prior to inputting it into a dPCR reaction, which is known in the art to assess individual partitions for a positive or negative signal. The PCR regents used by Jackson include multiple target-specific primers and fluorescent probes, for both mutant and wild-type targets [p237, col2, para3]. Jackson’s results demonstrated how “the mutant fraction detected in dPCR after pre-amplification is highly representative of the actual mutant allele frequency in the original sample [p243, col1, para1].”
Claims 12-14 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Jackson in view of Coccaro and further in view of Saal [US 2018/0340230 A1].
Jackson and Coccaro teach the limitations of claim 11 as described above.
However, they do not teach the use of asymmetric incremental amplification (as described in claims 12-14) in the pre-amplification step, nor the use of the same primer set in both the pre-amplification step and the exponential amplification step (as described in claim 18).
Saal teaches a method of detection for low-abundance variants in which an asymmetric incremental polymerase reaction is followed by an exponential PCR [Saal, abstract].
In this method, a set of primers comprising at least a primer-H and a primer-L is provided in which the melting temperature of primer-H is at least 15oC higher than that of primer-L (which would be included in the limitation of a difference of 10oC or higher of the instant application). The primers are designed so that primer-L is complementary to the extension product of primer-H. When the sample is first thermocycled, it is done at high temperatures so that primer-H anneals and extends, but primer-L does not [Saag, pg3 [0027]]. A second amplification is then performed at a lower temperature so that both primer-H and primer-L are able to function (note: the primers used for this amplification are the same as in the first amplification) [Saal, pg3 [0033]].
Saal explains that exponential amplification of low-abundance variants can result in PCR errors early on in the process which would result in false positive results, thus impeding the detection of true positive samples. According to Saal, asymmetrical incremental amplification overcomes this issue by reliably giving a consistent signal advantage to true-positive reactions over false-positive reactions [Saal, pg1 [0007-9]]. This signal advantage acts as a “head-start” for true positive reactions so that there is a distinguishable difference between true-positive reactions and false-positive reactions [Saal, pg2 [0015-16]].
Therefore, it would have been obvious to one of ordinary skill in the art prior to the effective filling date of the claimed invention to use the asymmetrical incremental amplification step of Saal for the pre-amplification step of Jackson and Coccaro as this would result in a method for cancer-relevant mutation detection that is able to overcome the pitfalls that occur when performing the pre-amplification with exponential PCR.
Applying a known technique to a known device (method or product) ready for improvement to yield predictable results is likely to be obvious. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, D.).
Response to Arguments
Applicant's arguments filed 26 January 2026 have been fully considered but they are not persuasive.
Regarding the rejections under 35 USC § 103, Applicant’s arguments and Examiner’s responses are below:
Argument 1:
Summary:
Jackson does not report a method for the detection of structural variants which are under-represented in a sample. Jackson instead performs pre-amplification on point mutations chosen because they are known in the art, not because they are identified as underrepresented. Coccaro does not report a pre-amplification step nor the identification of under-represented structural variants. Instead, Coccaro describes a study in which a known, common fusion gene is monitored. Therefore, the combination of the two references would not arrive at the claimed invention as both are missing elements.
Response:
While Jackson does not detect structural variants, point mutations (known or unknown) would be under-represented in a sample when compared to the wild-type. Jackson states right in the abstract: “First, mutant allele fractions are typically low in a large background of wild-type circulating, cell-free DNA.” Therefore, Jackson is telling one of ordinary skill in the art that her method is for detecting underrepresented targets. Any sample which has not been enriched for mutant DNA, would contain two fractions: a wild-type fraction and a mutant fraction. A skilled artisan would recognize that the mutant fraction would be present in a lesser amount than the wild-type fraction, particularly in cfDNA.
Regarding Coccaro, the study being described monitors (aka detects) the presence of a fusion gene. While the fusion gene is known in the art, it would still be under-represented in a sample of circulating, cell-free DNA when compared to the wild-type, for the same reason as described above. Furthermore, a skilled artisan would know that a fusion gene is a type of structural variant.
Therefore, the invention resulting from detecting the target of Coccaro with the method of Jackson would involve the pre-amplification of an under-represented structural variant.
Argument 2:
Summary:
Neither Jackson nor Coccaro report a quantification step in which (1) partition counts AND (2) a measure of the increase yielded by pre-amplification (amplification factor) are used to determine the original sample concentration.
Response:
As discussed in the initial rejection, Jackson used dPCR to analyze a sample, which inherently involves counting positive and negative partitions (1). Regarding (2), while Jackson does admit that additional testing would be required to perform absolute quantification, in reviewing their data to determine if amplification bias was evident, they found that the targets were amplified 29 to 33-fold when compared to the pre-amplified targets. Therefore, Jackson is determining relative quantification of the different targets (i.e. the quantity of each target in relation to the others), and is determining the amount of increase in pre-amplified targets in relation to the non-pre-amplified targets (i.e., “a measure of the increase of the abundance of the copies of the selected [targets] yielded by the pre-amplification”) to show that there was no significant amplification bias in the pre-amplification, thus validating the technique. As the claim language does not require the determination of absolute quantification, any form of quantification (including the relative quantification of Jackson) would read on the claimed invention. Furthermore, as the claim does not limit how the “measure of the increase of the abundance” is “used” in determining the quantities of the targets, Jackson meets these limitations.
Argument 3:
Summary:
Saal performs pre-amplification to address “polymerase error false positives in SNV detection”, whereas the instant application uses pre-amplification to address “stochastic loss of rare targets during partitioning and sample loss in dead volumes” in the detection of structural variants.
Response:
Per MPEP 2144.IV:
The reason or motivation to modify the reference may often suggest what the inventor has done, but for a different purpose or to solve a different problem. It is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by applicant. See, e.g., In re Kahn, 441 F.3d 977, 987, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006) (motivation question arises in the context of the general problem confronting the inventor rather than the specific problem solved by the invention); Cross Med. Prods., Inc. v. Medtronic Sofamor Danek, Inc., 424 F.3d 1293, 1323, 76 USPQ2d 1662, 1685 (Fed. Cir. 2005) ("One of ordinary skill in the art need not see the identical problem addressed in a prior art reference to be motivated to apply its teachings.")
Response Summary:
Applicant’s arguments are not persuasive because obviousness is not negated simply because there was a different reason in the prior art for combining teachings of the references.
Conclusion
THIS ACTION IS MADE FINAL. 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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/K.N.K./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681