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 .
Election/Restrictions
Applicant’s election without traverse of group II, claims 1-5, 7, 12-15 and species chromosome 22 nucleotide 29062500-29070000 in the reply filed on 06/08/2026 is acknowledged.
Claims 6, 8-11, 16-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/08/2026.
Claims 1-5, 7, 12-15 are under examination. Chromosome 22 nucleotide 29062500-29070000 are under examination for claim 7.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-5, 7, 12-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 and 12 recites “novel tumor marker” which renders the claim indefinite. It is unclear what is encompassed by novel as once the tumor marker is identified is it no longer novel. Additionally, the scope of the claims is indefinite as the scope would change over time based on what is a known tumor marker. While the claim requires tumor marker to be novel it is unclear what is required to be a novel tumor marker and one of ordinary skill in the art would not be apprised of infringing on the claimed method. Accordingly the recitation of a novel tumor marker renders the claim indefinite. This rejection could be overcome by deleting the term “novel” in the claims.
Claim 1, 3, and 5 recite “potential structural variant”. The recitation of “potential” renders the claim indefinite. It is unclear if the limitations following potential are part of the claimed invention. It is unclear if the claim is requiring a structural variant is part of the genomic region that is sequencing or if the claim does not require the structural variant to be part of the region. The recitation of potential without requiring positively identifying or determining a structural variant renders the claim indefinite as to whether this is required for the claim. Additionally it is unclear how sequencing a potential variant without requiring a variant present will provide a tumor marker or comprises a method of tumor marker analysis. While the claim requires potential structural variant, it is unclear what is required to be a potential SV and one of ordinary skill in the art would not be apprised of infringing on the claimed method. Accordingly the recitation of a potential structural variant marker renders the claim indefinite.
Claim 12 recites “SV is characterized by a region of at least 20 nucleotides at either site of the SV’s associated chromosomal breakpoint”. It is unclear what this limitation encompasses. It is unclear if the claim is requiring two different structural variants, two different sites within the chromosome, two different break sites in the chromosome or some other site within the chromosomal. The recitation of “either” without indicating any sites, including two different sties renders the claim indefinite as it is unclear what the site is.
Claims 2-5, 7 depend from claim 1 and 13-15 depend from claim 1 and claim 12 and are indefinite for the reasons applied to claim 1 and claim 12.
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, 7, and 12-15 rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and a law of nature without significantly more.
Claims 1 and claim 12 recite a law of nature/natural phenomenon. Claim 1 recite a method for tumor analysis and claim 12 recites a method for monitoring tumor progression in a patient. Claim 1 and claim 12 recite sequencing genomic region surrounding a potential structural variant to provide one or more novel tumor markers specific for a tumor of a patient and identifying a tumor mark specific for a tumor. The structural variants associated with a tumor and tumor marker are a natural phenomenon that exists apparat from any human action. This type of correlation is a consequence of a natural process.
Claim 1 recites preselecting a chromosomal region on genomic and providing a novel tumor marker that are specific for said tumor of the patient. Claim 12 recites identifying one or more novel tumor markers that are specific for said tumor of the patient, analyzing the first biopsy for presence of SV, analyzing second biopsy, and recording and comparing the presence of SV in the two biopsies. The recitation of preselecting and providing a novel tumor marker encompasses a data analysis process that can be practiced in the mind. It is noted that preselecting is not limited and can broadly encompass a mental analysis step that includes selecting a region. The recitation of identifying and analysis is a mental process. Neither the claims nor the specification set forth limiting definitions for identifying and analyzing and the claims do not set forth how identifying and analyzing is accomplished. The broadest reasonable interpretation of identifying and analyzing is a step that be accomplished mentally by evaluating data and critical thinking processes wherein on mentally reads information and makes a conclusion by identifying SV and presence of SV.
These judicial exceptions are not integrated into a practical application because the claims do not recite additional steps or elements that integrate the recited judicial exceptions into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the steps in addition to the judicial exception are data gathering steps recited at a high level of generality employing techniques that were well-established, routine and conventional at the time of the invention. 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 3-5 recite the step of preselecting is performed by capturing and isolating , TLA and genomic region is sequenced by third generation sequencing, these techniques were well known, routine and conventional in the art as taught by Pradhan (Scientific Reports, 7:14521, pp 1-12) and de Vree (Nature Biotechnology, vol 32, p1019-1027).
Claims 2 and 13 recite a tissue and liquid biopsy, this further limits the sample and thus is a field of use limitation and does not amount to significantly more.
Claim 7 recites potential SV comprises a region of chromosome 22 nucleotide 29062500-29070000. This claim only limits the sequences that are identified and thus only limit the judicial exceptions. However it was routine in the art to determine SV in Chromosome 22 nucleotide 29062500-29070000 as taught by Pradhan (Scientific Reports, 7:14521, pp 1-12).
Claim 14 and 15 recite therapy. While claim 15 recites therapy is selected from surgery, chemotherapy, radiation therapy, targeted therapy, immunotherapy, stem cell or bone marrow transplant, hormone therapy or combination thereof, these therapies is not particular, i.e. specifically identified so that it does not encompass all applications of the judicial exception. Additionally the treatment limitations do not appear to have a significant relationship to the exception.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. 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. Thus the prior art and specification demonstrates it was routine, well-known and conventional in the art to determine structural variants in tumor markers. 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.
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 1-3, 5, and 7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pradhan (Scientific Reports, 7:14521, pp 1-12).
Pradhan teaches obtaining tumor samples from FFPE (see samples) (claim 2). Pradhan teaches isolating genomic DNA, digesting and ligation of DNA to capture and isolate chromosomal regions (preselecting chromosomal region)(see digestion and ligation of DNA) (claim 3). Pradhan teaches sequencing using MiniION (nanopore sequencing, third generation sequencing) (see LDI-PCR) (claim 5). Pradhan teaches SV in TTC28 including the 3’ end of TTC28. Pradhan teaches the 3’ end comprises chr22:29065455-29066124 (claim 7) (see whole genome sequencing analysis and fig 1). Therefore, Pradham teaches providing genomic DNA, preselecting chromosomal region comprising at least part of a potential structural variant, and sequencing the region by nanopore sequencing to provide tumor markers (see fig 1 and material and methods).
Claims 1-3 and 12-15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Mayrhofer (Genome Medicine, 2018, 10:85, pp 1-13).
Mayrhofer teaches obtaining blood samples and fixed tumor tissue samples from prostate cancer patients (see methods) (claim 2 and 13). Mayrhofer teaches sequencing and hybridization capture targeted sequencing was performed (see pg. 3, 2nd column) (claim 3)(preselecting a chromosome region). Mayrhofer teaches sequencing was performed and identified structural variations in the human genome (sequencing the genomic region around potential structural variant to provide novel tumor markers). Mayrhofer teaches identifying SNP and genomic structural rearrangements. Mayrhofer teaches providing a first and second biopsy at different times and analyzing the first and second biopsy for presence of structural variants, recording and comparing (See clonal dynamics during treatment pg. 5, fig 1, fig 5) (claim 12-13). Mayrhofer teaches obtaining sample before and after treatment of abiraterone therapy (see pg. 5, 1st column) (claim 14-15).
Claims 1, 4-5 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by de Vree (Nature Biotechnology, vol 32, p1019-1027)
De Vree teaches providing genomic DNA from breast tumor tissue from breast cancer cases (see sample collection). De Vree teaches targeted locus amplification followed by sequencing genomic region (see TLA sample preparation and TLA data) (claim 4). De Vree teaches using TLA to sequence clinically relevant genes to search for structural variants in or near the sequences (see structural variants and gene fusions in cancer samples). De Vree teaches providing genomic DNA sample from tumor cells, performing TLA to preselect chromosomal region and sequence the genomic region to identify structural variants.
Conclusion
No claims are allowable.
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
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