DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims Status
Claims 1-6 are pending.
Claims 1-6 are examined.
Priority
The instant application claims priority to US provisional Application No. 63/162665, filed 03/18/2021. It is noted that the provisional application No. 63/162665 does not provide support for filtering the plurality of SVs.
Therefore, the Effective Filing Date (EFD) assigned to each of the claims 1, 2, and 4-6 is the provisional filing date of Application 63/162665, filed 03/18/2021. The EFD assigned to claim 3 is the instant filing date of 03/18/2022.
Information Disclosure Statement
The Information Disclosure Statement filed 06/02/2025 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copies of the IDS documents are included with this Office Action.
It is noted that certain references lack appropriate page numbers as is required under 37 CFR 1.97. The Examiner has annotated the references herein. Applicant is kindly reminded to provide proper citations in compliance with 37 CFR 1.97 in all future submission to the office. Furthermore, the Foreign Reference is not considered as there is no submitted copy. The Transmittal letter dated 06/02/2025 does not give the Application Number in which the reference was supposed to be previously submitted.
Drawings
The drawings filed 07/20/2022 are accepted.
Specification
The disclosure is objected to because of the following informalities:
In paragraph [0109], “the terms ‘machine-readable medium’ ‘computer-readable medium’ refers” should read “the terms ‘machine-readable medium’ and ‘computer-readable medium’ refer”
In paragraph [0124], “was used as described below.Retrospective samples” should “was used as described._Retrospective samples”
In paragraph [0128], “genomewide” should “genome-wide”
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Objections
Claims 1-3 are objected to because they include reference characters which are not enclosed within parentheses.
Reference characters corresponding to elements recited in the detailed description of the drawings and used in conjunction with the recitation of the same element or group of elements in the claims should be enclosed within parentheses so as to avoid confusion with other numbers or characters which may appear in the claims. See MPEP § 608.01(m).
Claim 1 is objected to because of the following informalities:
The acronyms “AML” and “MDS” are not defined within the claims
Appropriate correction is required.
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 1-6 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims recite a method.
With respect to step (2A)(1): The claims recite abstract ideas of mental processes.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claim 1:
performing a structural variant analysis on the whole-genome sequencing dataset, the structural variant analysis including copy-number alteration (CNA) identification, structural variant (SV) identification, and gene-level variant identification to identify clinically relevant structural variants indicative of AML or MDS within the whole-genome sequencing dataset
producing a report comprising the clinically relevant CNAs, SVs, and gene0level variants identified by the structural variant analysis
Dependent claims 2-5 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 1, and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 2: “transforming […] the alignments of the whole-genome sequencing dataset into a plurality of read counts over 500,000 bp nonoverlapping windows across the genome”; “transforming […] the plurality of read counts into a plurality of CNAs”; “filtering […] plurality of CNAs to retain only CNAs greater than 5Mbp”
Claim 3: “transforming […] the alignments of the whole-genome sequencing dataset into a plurality of SV calls”; “filtering […] the plurality of SVs to retain only SV calls greater than 100 kbp in length”; “filtering […] the SV calls greater than 100 kpb in length to identify translocations, deletions, duplications, and inversions that overlap a predefined list of recurrent and/or risk-defining SVs associated with AML or MDS”
Claim 4: “identifying […] the alignments of the whole-genome sequencing dataset within about 85kbp targeting 40 predetermined genes and gene hotspots that are recurrently mutated in AML or MDS”
Claim 5: “wherein the clinically relevant CNAs, SVs, and gene-level variants identified by the structural variant analysis are indicative of a clinical outcome of the subject”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than analyzing DNA sequences in order to identify differences indicative of a disease diagnosis.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claim 1 recites the following additional elements that are not abstract ideas:
computer-implemented
providing a whole-genome sequencing dataset
The step of providing a whole-genome sequencing gathers the data on which the judicial exceptions are performed and is thus directed to data gathering. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). The element of the method being computer-implemented is directed to applying the method to a generic computer. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)).
Dependent claim 6 is directed to a step of data gathering as it describes the method of gathering the sequencing data on which the judicial exceptions are performed.
None of these dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d)(I), determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claim 1: The additional element of a computer-implemented method, and providing whole-genome sequencing dataset do not rise to the level of significantly more than the judicial exception. With respect to the generic computer elements, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). Furthermore, with reference to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is also a routine and conventional activity. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 6: The additional element of performing whole-genome sequencing on a biological sample comprising tumor DNA from the subject with about 60x genome coverage does not rise to the level of significantly more than the judicial exception. The prior art Desai et al. (“Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data”, PLOS One, 2013) discloses current Next Generation Sequencing that can easily achieve 60X to 100X coverage for large genomes (page 1, column 2, paragraph 2). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
In combination, the collection or generation of the data, acted upon by the judicial exception, fail to rise to the level of significantly more. The data gathering steps provide the data for the judicial exception. No non-routine step or element has clearly been identified.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 5, and 6 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Landau et al. (US 2021/0002728 A1, published January 7, 2021).
Regarding claim 1, Landau et al. teaches a method of identifying structural variants in a subject with AML (paragraph [0065]) comprising:
providing a whole-genome sequencing dataset, the whole-genome sequencing dataset comprising a plurality of alignments of tumor DNA sequence fragments to a reference human genome to a computing device (paragraph [0017]);
performing a structural variant analysis on the whole-genome sequencing dataset, the structural variant analysis including copy-number alteration (CNA) identification, structural variant (SV) identification, and gene-level variant identification (paragraph [0018]) to identify clinically relevant structural variants indicative of AML or MDS within the whole-genome sequencing dataset (paragraph [0065]); and
producing a report comprising the clinically relevant DNAs, SVs, and gene-level variants identified by the structural variant analysis: Landau et al. teaches producing a report of the identified CNVs for further clinical applications such as tumor fraction estimation (Figure 8).
Furthermore, Landau et al. teaches the methods being performed by a computer system (paragraph [0037], [0038], and the like).
Regarding claim 5, the claim is directed to the clinically relevant CNAs, SVs, and gene-level variants identified by the structural variant analysis are indicative of a clinical outcome of the subject. Landau et al. teaches the method of claim 1. Landau et al. also teaches that the somatic alterations in cfDNA of a subject such as copy number variation, tandem repeats, gene mutations, etc. are indicators of pathogenic processes or pharmacological response to a therapeutic intervention (paragraph [0075]).
Regarding claim 6, the claim is directed to performing whole-genome sequencing on a biological sample comprising tumor DNA from the subject with about 60x genome coverage. Landau et al. teaches the method of claim 1. Landau et al. also teaches performing whole-genome sequencing at a coverage of 70x or more (paragraph [0092]).
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 2-4 are rejected under 35 U.S.C. 103 as being unpatentable over Landau et al., as applied to claims 1, 5, and 6 in the 102 rejection above, in view of Rava et al. (US 10388403 B2, published August 2019, IDS reference).
Regarding claim 2, the claim is directed to transforming the alignments of the whole-genome sequencing dataset into a plurality of read counts over 500,000 bp nonoverlapping windows across the genome; transforming the plurality of read counts into a plurality of CNAs; and filtering plurality of CNAs to retain only CNAs greater than 5 Mbp. Landau et al. teaches the method of claim 1. Landau et al. also teaches calling CNVs segments or SV calling that exceed a threshold length preferably greater than Mbps (paragraph [0034]) and Landau et al. teaches that CNVs or SVs are at least 5 Mbps in cumulative size or larger (paragraph [0022]).
Landau et al. does not teach the claim element of transforming the alignments of the whole-genome sequencing dataset into a plurality of read counts over 500,000 bp nonoverlapping windows.
However, Rava et al. teaches identifying aneuploidy by binning sequences into blocks wherein the block length is 1 million base pairs, or potentially 100kb, etc. and these lengths do not overlap. The blocks are analyzed to identify aneuploidy (column 144, line 31).
Regarding claim 3, the claim is directed to transforming the alignments of the whole-genome sequencing dataset into a plurality of SV calls; filtering the plurality of SVs to retain only SV calls greater than 100 kbp in length; and filtering the SV calls greater than 100 kbp in length to identify translocations, deletions, duplications, and inversions that overlap a predefined list of recurrent and/or risk-defining SVs associated with AML or MDS. Landau et al. teaches the method of claim 1. Landau et al. also teaches calling CNVs segments or SV calling that exceed a threshold length preferably greater than Mbps (paragraph [0034]) and Landau et al. teaches that CNVs or SVs are at least 5 Mbps in cumulative size or larger (paragraph [0022]).
Landau et al. does not teach the claim element of identifying translocations, deletions, duplications, and inversions that overlap a predefined list of recurrent and/or risk-defining SVs associated with AML or MDS.
However, Rava et al. teaches identifying aneuploidies in regions comprising preselected genes, such as oncogenes or tumor suppressor genes (column 18, line 18).
Regarding claim 4, the claim is directed to identifying the alignments of the whole-genome sequencing dataset within about 85 kbp targeting 40 predetermined genes and gene hotspots that are recurrently mutated in AML or MDS. Landau et al. teaches the method of claim 1.
Landau et al. does not teach the claim element of 40 predetermined genes and gene hotspots that are recurrently mutated in AML or MDS.
However, Rava et al. teaches identifying aneuploidies in regions comprising preselected genes, such as oncogenes or tumor suppressor genes (column 18, line 18). Rava et al. teaches probes with an average interprobe distance of 5.8 kb, and finding 49 cancer genes directly encompasses or overlapped by copy number variations (column 91, line 7).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have incorporated the predetermined markers of Rava et al. to the method of Landau et al. because Landau et al. is directed to detecting residual tumor disease in human cancer patients (Abstract) using structural markers such as copy number variations (paragraph [0008]) and Rava et al. is also directed to analysis of copy number variations of a sequence in a sample to determine structural variations associated with medical conditions such as cancer (Abstract). Thus, one of ordinary skill in the art would have a reasonable expectation of identifying known marker copy number variations in a patient’s sample in order to detect cancer.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 4 of copending Application No.18/316,294. Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of Application No. ‘294 encompass the instant claims.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Instant Claims
Application No. 294
Claim(s)
Limitations
Claim(s)
Limitations
1
A computer-implemented method for the identification of clinically relevant structural variants in a subject with AML or MDS from whole genome sequencing data, the method comprising: a. providing a whole-genome sequencing dataset, the whole-genome sequencing dataset comprising a plurality of alignments of tumor DNA sequence fragments to a reference human genome to a computing device; b. performing, using the computing device, a structural variant analysis on the whole-genome sequencing dataset, the structural variant analysis including copy-number alteration (CNA) identification, structural variant (SV) identification, and gene-level variant identification to identify clinically relevant structural variants indicative of AML or MDS within the whole- genome sequencing dataset; and c. producing, using the computing device, a report comprising the clinically relevant CNAs, SVs, and gene-level variants identified by the structural variant analysis
1
A method of detecting residual disease in a subject having or suspected of having a urinary tract-associated cancer, the method comprising: obtaining a urine sample from the subject; extracting cell-free DNA (cfDNA) from the urine sample; detecting a cfDNA-derived metric using ultra-low-pass whole genome sequencing (ULP-WGS) and next-generation sequencing (NGS); wherein the cfDNA-derived metric comprises at least one of a tumor fraction (TFx) value, a variant allele frequency (VAF) value and a tumor mutational burden (TMB) value; and determining the subject to have residual disease or no residual disease based on the cfDNA-derived metric.
4
wherein detecting the cfDNA-derived metric further comprises detecting single nucleotide variants (SNVs) or copy number alterations (CNAs) in the cfDNA
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILIE A NEULEN whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.N./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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