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 .
Claim Status
Currently, claims 1-10, 19-21 are pending in the instant application. Claim 11-18 have been canceled and claims 6, 19-21 are withdrawn. This action is written in response to applicant's correspondence submitted 06/17/2025. All the amendments and arguments have been thoroughly reviewed but were found insufficient to place the instantly examined claims in condition for allowance. The following rejections are either newly presented, as necessitated by amendment, or are reiterated from the previous office action. Any rejections not reiterated in this action have been withdrawn as necessitated by applicant' s amendments to the claims. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action. This action is Final.
Claims 1-5 and 7-10 are under examination. Claims 1-5 and 7-10 are under examination with respect to SCNA.
Withdrawn Rejections
The objection to claims 3 and 7 is withdrawn in view of the amendment to the claims.
The rejection of claims 3, 7, 11-15 under 35 USC 112(b) is withdrawn in view of the amendment to the claims.
The rejection of claims 11-16 under 35 USC 112(a) is withdrawn in view of the amendment to the claims to cancel claims 11-16.
Oath/Declaration
The affidavit under 37 CFR 1.130(a) filed 06/17/2025 is insufficient to overcome the rejection of claims 1, 4-5, 7-10 based upon Berry et al. (2017) as set forth in the last Office action because the declaration fails to provide an unequivocal statement from one or more joint inventors that he/she/they invented the potential prior art subject matter and a reasonable explanation of the presence of additional authors/inventors oof the potential prior art subject matter (see MPEP 717.01(a)(1)). The declaration filed on 6/16/2025 merely states the other authors on Berry et al (2017) are not co-inventors of the subject matter claimed in the above-identified application. There is no reasonable explanation of the presence of the additional authors on the publication by Berry et al (2017) and there is no statement that the inventors invented the potential prior art subject matter. A statement stated the other inventors are not co-inventors with no other explanation is not sufficient to overcome the rejection of record. Applicant has not provided an “unequivocal” statement from the inventor or joint inventor that he/she (or some specific combination of named joint inventors) invented the subject matter of the disclosure and Applicant has not provided a reasonable explanation of the presence of additional authors listed on the Berry et al (2017) reference.
Maintained Rejections
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-5 and 7-10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. The claims recites a law of nature and abstract ideas. These judicial exceptions are not integrated into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. This rejection was previously presented and is rewritten to address the amendment to the claims.
The following inquiries are used to determine whether a claim is drawn to patent-eligible subject matter.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? Yes, all of the claims are directed to a process.
Step 2A. Is the claim directed to a law of nature, a natural phenomenon or an abstract idea (judicially recognized exception) and does the claim recite additional elements that integrate the judicial exception into a practical application?
Yes, the claims are directed to law of nature/natural phenomenon. Claim 1 recites prognosis or diagnosis and treating of retinoblastoma by assaying cfDNA from aqueous humor of the subject for somatic chromosomal copy number alterations (SCNAs). The claims include correlation between SCNA for prognosis or diagnosis of retinoblastoma and SCNA for treatment. The recited relationship is a natural phenomenon that exists apart from any human action. This type of correlation is a consequence of natural processes.
The claims also recite the judicial exception of an abstract idea and particularly mental processes. Claim 1 recites the abstract idea of a mental process. Claim 1 recites the step of “determining” a high likelihood or severity of retinoblastoma. Claim 3 requires wherein the gain in SCNA is statistically significantly higher than that of a control. Neither the specification or the claims set forth limiting definition for determining or shows a response and the claims do not set forth how determining or shows a response correlating with clinical response is accomplished. The broadest reasonable interpretation of the determining and showing is a step that can be accomplished mentally by evaluating data and critical thinking process wherein one mentally reads information in a database or report then draws a mental conclusion. Such “determining” thereby encompasses process that may be performed mentally and this is an abstract idea.
Having determined that the claims recite a judicial exception, it is then determined whether the claims recite additional elements that integrate the judicial exception into a practical application.
The claims do not recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s). For example, the claims do not practically apply the judicial exception by including one or more additional elements that the courts have stated integrate the exception into a practical application:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
An additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
An additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
An additional element effects a transformation or reduction of a particular article to a different state or thing; and
An additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological
environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception.
While claim 1 recites a step of treating, the step of treating only occurs if at least one chromosome has a gain in SCNA, therefore this treatment is a conditional step, occurring only if a chromosome gain has occurred. The claims do not require that a chromosome gain is detected only that the cfDNA is assay for a chromosome gain, however this encompasses not detecting a chromosome gain and not treating a subject. For example the claims do not require detecting an increase in SCNA in a subject and then administering to the subject with the increased SCNA with a specific therapy to treat retinoblastoma.
As mentioned above, a claim limitation can integrate a judicial exception by applying or using the judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition. When evaluating this consideration one must the following:
(i) the particularity or generality of the treatment or prophylaxis limitation;
(ii) whether the limitations have more than a nominal or insignificant relationship to the exception; and
(iii) whether the limitations are merely extra solution activity or field of use.
The steps of treating in claim 1 is conditional and do not occur based on the judicial exception i.e., specifically identified so that it does not encompass all applications of any type of therapy and are applied based on the judicial exception. In other words the treatment only occurs if at least one chromosome has a gain. Additionally the treatment limitations do not have a significant relationship to the exception. For these reasons the therapeutic treatment does not integrate the judicial exceptions into a practical application.
In addition to the judicial exceptions the claims recite gain of chromosome 6p (claim 4-5) and statistically significant gain in SCNA (claim 3). Claim 2 recites controls. Claims 8-9 recite timing of the therapeutic treatment. Claim 10 recites shallow genome sequencing. These additional steps/elements are not considered to integrate the judicial exception into a practical application because they merely add insignificant extra-solution activity (data gathering) to the judicial exception.
Step 2B - Does the claim recite additional elements that amount to significantly more than the judicial exception? No.
Herein the claims as a whole are not considered to recite any additional steps or elements that amount to significantly more than well-understood, routine, and conventional activities in the art and do not add something “significantly more” so as to render the claims patent-eligible. The step of obtaining a cell free DNA from aqueous human and determining gain in SCNA in chromosome 6p merely instructs a scientist to use well established, routine and conventional nucleic acid techniques to gather samples for diagnostic analysis.
The step of determining SCNA in aqueous humor constitutes a data gathering step required to apply the law of nature/natural phenomenon. It is acknowledged that the claims name particular chromosome, gain in 6p, however the claims do not require a particular, non-conventional primer or probe consisting of or comprising a specific nucleotide sequence or any other specific reagent that is used to accomplish such determining such that the claims would recite significantly more than the judicial exception. The targets to be detected are part of the judicial exception and thereby the naming of the targets does not add something “significantly more” to the recited judicial exceptions.
The additional steps and elements are recited at a high degree of generality and are all routine, well understood and conventional in the prior art. The recited steps and elements do not provide inventive concept necessary to render the claims patient eligible. There is no combination of elements in this step that distinguishes it from well-understood, routine and conventional data gathering activity engaged in by scientists prior to applicant’s invention and at the time the application was filed. Many cited prior art references in this record demonstrate that these techniques were conventional at the time of the invention. The prior art of Kooi (EBioMEdicine, 2015, 2, pp 660-670) teaches obtaining DNA samples from retinoblastoma samples and assaying for amplification of chromosome 6p in patients with retinoblastoma. Berry (2017, cited on IDS) teaches SCNA gain of chromosome 6p in aqueous humor of retinoblastoma samples. Lillington teaches SCNA gain of chromosome 6p in retinoblastoma samples. Berry et al (ARVO Annual Meeting Abstract, (2016), vol 57, 3669, pp 1-3) teaches DNA analysis of aqueous humor sample in retinoblastoma samples. Thus the prior art and specification demonstrates it was routine, well-known and conventional in the art to determine SCNAs in retinoblastoma samples, including assaying for gain of chromosome 6p in aqueous humor samples. Dependent claims 2-3 further limit the control and statistical analysis results. Claim 4-5 further describe the SCNAs. Claims 12 and 14-16 further describe the prior treatment. The dependent claims do not provide significantly more to the claims outside of the judicial exception as they encompass conventional techniques as described in the instant specification as noted above.
Response to Arguments
The response traverses the rejection on page 4 of the remarks mailed 06/17/2025. The response asserts that claim 1 has been amended to include treating the subject and this limitation imposes a meaningful limit on the judicial exception and integrates the recited judicial exception into a practical application. As addressed in the rejection above, the treating step in claim 1 is conditional. Treating only occurs if at least one chromosome has a gain in SCNA and the claim does not require positively identifying a gain in a chromosome and encompasses assaying any SCNA, including none. For these reasons and reasons of record the rejection is maintained.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 4-5 and 7-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Berry et al. (2017, cited on IDS). This rejection was previously presented and has been rewritten to address the amendment to the claims.
Berry teaches cell free DNA was isolated from 6 aqueous humor samples from children with retinoblastoma. Berry teaches 2 were after primary enucleation and 1 undergoing multiple intravitreous injection for vitreous seeding (see design, setting and participants). Berry teaches assaying cfDNA from AH followed by analysis using QIAseq Ultralow Input Library (smooth whole genome sequencing) (see next-generation sequencing) (claim 7 and 10). Berry teaches thresholds of 1.25 relative to a median were used using median-centered data and teaches amplitude gained more than 1.4 (see figure 2 and 3) (control has amplitude no more than 1.0) (claim 5) (see data analysis). Berry teaches gain in 6p (see pg. 1223, 2nd column) (claim 4). Berry teaches 6p gain in patient after primary enucleation in AH (see figure 1). Berry teaches gain of 6p chromosome in AH after systemic treatment plus intravitreous chemotherapy (see table, pg. 1225). Berry teaches one patient relapsed and was further treated with chemotherapy (aqueous humor taken at initial chemotherapy, at recurrence and at 1 month apart from therapy, first and second therapy, and conclusion of therapy) (claims 8-9 and 13-16). Berry teaches that copy number variation in cfDNA detected in AH is correlated with Rb tumors (see pg. 1226). Berry teaches DNA present in AH can be evaluated (See pg. 1229).
Response to Arguments
The response traverses the rejection on page 5-6 of the remarks mailed 06/17/2025. The response asserts the inventors Jessica Lee Berry, Liya Xu and James Bruce Hicks were co-authors on the reference Berry et la. (2017). The response asserts the other authors were names as co-authors on the paper but were not co-inventors of the subject matter claimed in the instant case. The response addresses disclosures of his or her own work within a year before application filing date can not be used against him or her under 35 USC 102(a) and points to MPEP 2132.01. It is noted that the rejection is not under 35 USC 102(a) but under AIA 102(a)(1). A 130(a) attribution is required and the declaration filed by Berry is insufficient to disqualify Berry et al (2017) for the reasons stated above. Applicant has not provided an “unequivocal” statement from the inventor or joint inventor that she/he/they invented the subject matter and has not provided a reasonable explanation of the presence of the additional authors listed on Berry et al (2017). A statement that they are co-authors but not co-inventors is not a reasonable explanation of the presence of the additional authors. See MPEP 717.01(a). For these reasons and reasons of record this rejection is maintained.
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.
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, 4, 7-9, are rejected under 35 U.S.C. 103 as being unpatentable over Lillington (Genes, Chromosomes & Cancer, 2003, 36, 121-128) in view of Berry et al (ARVO Annual Meeting Abstract, (2016), vol 57, 3669, pp 1-3)
Lillington teaches assaying retinoblastoma (Rb) tumors using comparative genomic hybridization. Lillington teaches gain of 6p was the most frequent event in Rb tumors. (see abstract). Lillington teaches tumor samples were obtained after enucleation and DNA was extracted from tumor samples (see tumor samples). Lillington teaches tumor DNA was assayed by CGH. Lillington demonstrates that patient tumors with metastasis detected 6p gain (see pg. 126, 1st column) (claim 9). Lillington teaches assaying increased SCNA at chromosome 6p in patients after treatment with chemotherapy (see table 1 and table 2) (claim 8, 11-12). Therefore Lillington teaches gain of SCNA is associated with retinoblastoma, severity of retinoblastoma and monitoring progression of retinoblastoma. Lillington teaches that patients classified as poor histo-prognostic risk amplification of chromosome 6 p was detected (see tumor samples and table 2 and results, pg. 124). Lillington teaches analysis of control DNA that does not have retinoblastoma (see CGH) (claim 2). Lillington does not teach analysis of aqueous humor samples.
Berry teaches obtaining aqueous humor of patients with retinoblastoma and assaying the aqueous humor for DNA and RNA. Berry teaches the aqueous humor of eyes with retinoblastoma harbor DNA, RNA and miRNA.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to modify the method of Lillington to use aqueous humor samples of the subject as taught by Berry to allow for more assessable, faster and more frequent sample collections. The ordinary artisan would have been motivated to use a sample from the subject comprising aqueous humor to eliminate the need for analyzing a tumor tissue sample. The ordinary artisan would have further been motivated to include an aqueous humor sample as taught by Berry to allow for analysis of retinoblastoma when a tumor tissue sample is not available and allow different collection times. The ordinary artisan would have had a reasonable expectation of success that analysis of SNCAs as taught by Lillington could be performed on aqueous humor of subjects with retinoblastoma because Berry teaches obtaining and analyzing DNA from aqueous humor of patients with retinoblastoma.
Claims 1-5, 7, are rejected under 35 U.S.C. 103 as being unpatentable over Kooi (EMioMedicine, 2015, vol 2, pp 660-670) in view of Berry et al (ARVO Annual Meeting Abstract, (2016), vol 57, 3669, pp 1-3).
Kooi teaches gain of genomic alterations in retinoblastoma tumor progression. Kooi obtaining retinoblastoma samples from tumor samples of primary enucleation (see patient samples) (without prior treatment). Kooi teaches extracting DNA from samples for copy number profiling. Kooi teaches copy number estimates were normalized, tumor sample and matched blood samples were normalized (control not comprising retinoblastoma) (median copy number gain) (claim 2). Kooi teaches detecting increased gain of 6p greater than 1.4 ratio and teaches p value under .05 (see 2.4 and pg. 666, 1st column) (claim 3-5). Kooi teaches increased frequencies of SCNAs at 6p cause malignant transformation (see pg. 668, 2nd column). Therefore Kooi teaches gain of SCNA is associated with retinoblastoma, severity of retinoblastoma and monitoring progression of retinoblastoma. Kooi does not teach analysis of aqueous humor of eyes with retinoblastoma.
Berry teaches obtaining aqueous humor of patients with retinoblastoma and assaying the aqueous humor for DNA and RNA. Berry teaches the aqueous humor of eyes with retinoblastoma harbor DNA, RNA and miRNA.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to modify the method of Kooi to use aqueous humor samples of the subject as taught by Berry to allow for more assessable, faster and more frequent sample collections. The ordinary artisan would have been motivated to use a sample from the subject comprising aqueous humor to eliminate the need for analyzing a tumor tissue sample. The ordinary artisan would have further been motivated to include an aqueous humor sample as taught by Berry to allow for analysis of retinoblastoma when a tumor tissue sample is not available and allow different collection times. The ordinary artisan would have had a reasonable expectation of success that analysis of SNCAs as taught by Kooi could be performed on aqueous humor of subjects with retinoblastoma because Berry teaches obtaining and analyzing DNA from aqueous humor of patients with retinoblastoma.
Claims 1 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Garcia-Chequer (Cancer Genetics, 2016, 209, 57-69) in view of Berry et al (ARVO, Annual Meeting Abstract, Sept 2016, vol 57, 3669).
Garcia-Chequer teaches obtaining DNA samples from retinoblastoma tumor samples (see DNA samples). Garcia-Chequer teaches assaying DNA from tumor samples for SCNAs by low whole genome sequencing (see illumine sequencing and expression microarray, pg. 59). It is noted the claim only requires determining a likehood or severity of retinoblastoma if at least one chromosome has a gain in SNCA, as such the determining step is conditional. In Garcia-Chequer, loss of SCNA are only identified and therefore meets this limitation of the claim as a gain of SCNA is not identified to determine retinoblastoma. Garca-Chequer does not teach assaying cell-free DNA from aqueous humor of a subject.
Berry teaches obtaining aqueous humor of patients with retinoblastoma and assaying the aqueous humor for DNA and RNA. Berry teaches the aqueous human of eyes with retinoblastoma harbor DNA, RNA and miRNA.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to modify the method of Garcia-Chequer to use aqueous humor samples of the subject as taught by Berry to allow for a more assessable sample, faster and more frequent sample collections. The ordinary artisan would have been motivated to use a sample from the subject comprising aqueous humor to eliminate the need for analyzing a tumor tissue sample. The ordinary artisan would have further been motivated to include an aqueous humor sample as taught by Berry to allow for analysis of retinoblastoma when a tumor tissue sample is not available. The ordinary artisan would have had a reasonable expectation of success that analysis of low genome sequencing as taught by Garcia-Chequer could be performed on aqueous humor of subjects with retinoblastoma because Berry teaches obtaining and analyzing DNA from aqueous humor of patients with retinoblastoma.
Response to Arguments
The response addresses all of the 103 rejections together in the response mailed 06/17/2025 (pages 6-7). The response asserts that none of the primary references mention the aqueous humor of the eye. The response asserts that Berry (2016) only discloses that the aqueous humor of eyes with Rb harbor DNA, RNA and miRNA and that changes in concentration of nucleic acid occur after treatment. The response asserts that Berry does not disclose if DNA, RNA, or miRNA has any correlation to Rb and the DNA, RNA, and miRNA in the aqueous humor may have nothing to do with Rb. The response further asserts there is no reasonable expectation that one of ordinary skill in the art would be able to detect and analyze the specific occurring in DNA, RNA, and miRNA in aqueous humor that correlated with Rb as the amounts of the specific components that correlate with Rb could be too low.
This response has been thoroughly reviewed but not found persuasive. Berry teaches the ability to measure DNA, RNA and miRNA from aqueous humor of subjects with Rb. While Berry does not teach the specific DNA, RNA or miRNA that was detected, Berry does demonstrate the ability to detect DNA, RNA and miRNA in aqueous humor. Based on the general knowledge available to one of ordinary skill in the art, the ordinary artisan would have been motivated to obtain aqueous humor sample from subjects with Rb and assay the aqueous humor for cell free DNA. Furthermore, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely that product [was] not of innovation but of ordinary skill and common sense. See KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In the instant case, assaying aqueous humor for cell free DNA is within the technical grasp of an ordinary artisan based on the teachings of Berry. Additionally, it was known in the art that biomarkers for retinoblastoma could be detected in aqueous humor. Shehata (Clin Biochem 2010 43:362-366) teaches measuring Survivn levels in aqueous humor samples of retinoblastoma and was determined to be correlated with tumor stage (see results). As such it was known in the art that biomarkers could be detected in aqueous humor that are related to Rb. Because the art demonstrates biomarkers detected in aqueous humor that are related to Rb, the ordinary artisan would have been motivated with an expectation of success that SCNA chromosome 6 gains could be assayed in aqueous humor of patients with Rb because the prior art demonstrates chromosome 6 SCNA gains are associated with Rb and Berry demonstrates the ability to measure DNA in aqueous humor of Rb patients. Therefore, absence secondary consideration such as evidence demonstrating the unpredictability of measuring cfDNA in aqueous humor that is associated with Rb, the ordinary artisan would have modify the teachings of Lillington, Kooi, and Garcia-Chequer and include analysis of aqueous humor samples to allow for a more assessable, faster and more frequent sample collection analysis of Rb. This should not be construed as an invitation for providing evidence, see MPEP 716.01 regarding the timely submission of evidence. For these reasons and reasons of record this rejection is maintained.
Conclusion
No claims are allowable.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SARAE L BAUSCH whose telephone number is (571)272-2912. The examiner can normally be reached M-F 9a-4p.
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/SARAE L BAUSCH/Primary Examiner, Art Unit 1699