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 .
Status of the application
This application has a filing date of 12/15/2023. No claim to priority has been asserted, accordingly domestic benefit is afforded to the filing date of the instant application.
Claims 1-26 are pending. In response to the restriction requirement mailed 3/13/2026, an election was made without traverse on 4/14/2026 to prosecute Group I, claims 1 and 3-22 and a species for search purposes was made to whole exome sequencing (WES). Claims 2 and 23-26 are withdrawn from further prosecution as drawn to a non-elected invention.
After a careful review of the prior art, the species election is withdrawn, and the instant application is thus examined within the scope of the claims.
Claim interpretation
Prior to analysis of the art, the claims must be construed. As noted in MPEP 2111, citing Phillips v. AWH Corp., 415 F.3d l303, 75 USPQ2d l321 (Fed. Cir. 2005), "During patent examination, the pending claims must be 'given their broadest reasonable interpretation consistent with the specification.' "
As pointed out in In re Mott, 190 U.S.P.Q. 536 (CCPA 1975), "Claims must be given broadest reasonable construction their language will permit in ex parte prosecution, and applicant who uses broad language runs the risk that others may be able to support the same claim with a different disclosure."
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language considering the specification as it would be understood by one of ordinary skill in the art. Regarding the term “union sequencing” this is not a conventional term of art. The term is presented in the specification 86 times without a limiting definition. First presented at paragraph [0005] the term is observed to mean “…combining the initial sequencing results of biological samples to yield union sequencing results; and scoring the predicted immunogenicity of neoantigens (e.g., one or more neoantigens) in the biological samples of the subject in need thereof based on the union sequencing results of the biological.” The closest term of art appears to be a “consensus sequence” as evidenced by the art of record. In the absence of a limited definition in the specification this term will be analyzed in terms of the metes and bounds of a consensus sequence.
35 USC 101
Claims 1 and 3–20 are rejected under 35 U.S.C. § 101 as being directed to patent-ineligible subject matter. (BRI)
Claim 1 is directed to the abstract idea of collecting, evaluating, and comparing information and making a decision based on that evaluation. Specifically, claim 1 recites:
preparing biological samples,
nucleic acid sequencing to obtain initial sequencing results,
evaluating those results by analyzing sequencing parameters,
based on that analysis, either combining the results into union sequencing results or selecting a representative biological sample, and
scoring predicted immunogenicity based on the resulting data.
This is an abstract data-analysis and decision-making process. The substantive focus of the claim is not an improvement to sequencing technology or to any other technology, but rather the analysis of sequencing-derived information and selection of an output based on that analysis.
Under Step 2A, Prong One of the USPTO eligibility analysis, the claim recites a judicial exception in the form of an abstract idea, including a mental process and certain methods of organizing human activity/data analysis. See MPEP §§ 2106, 2106.04, 2106.04(a), and 2106.04(d).
Under Step 2A, Prong Two, the additional elements do not integrate the exception into a practical application. The recited steps of:
preparing biological samples, and
nucleic acid sequencing,
These steps are merely insignificant pre- and extra-solution activity and data-gathering steps. They are recited at a high level of generality and do not impose any meaningful technological limitation on the abstract analysis. The claims do not recite a specific improvement in sequencing hardware, sequencing chemistry, computational processing, or laboratory technique. Rather, the claims merely uses conventional sequencing output as input to the abstract decision of whether to combine results or select a sample.
The “union sequencing results” and “representative biological sample” limitations likewise do not add a practical application; they are simply outputs of the abstract comparison/selection decision.
Under Step 2B, the claims do not include an inventive concept sufficient to transform the abstract idea into patent-eligible subject matter. The recited sequencing, sample preparation, and scoring steps are generic and are claimed functionally without a specific technological improvement. Accordingly, the claims amount to no more than applying generic laboratory activity to an abstract information-processing concept.
Claims 3–20 add only further narrowing limitations concerning:
sample types,
sample source,
timing of collection,
particular sequencing parameters,
result types,
nucleic acid type,
sequencing techniques,
subsequent sequencing, and
neoantigen peptide length.
These additional limitations do not change the fundamental character of the claims. They continue to recite the same abstract data-analysis and decision-making concept, implemented with routine laboratory and informational steps, without a meaningful technological improvement or other practical application. Therefore, claims 3–20 are also rejected under 35 U.S.C. § 101.
Prior art
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 and 3–22 are rejected under 35 U.S.C. § 103 as being unpatentable over WO 2014/151117 in view of WO 2020/221783 and US 12,545,963.
Regarding claim 1, WO 2014/151117 teaches obtaining tumor nucleic acid and genomic nucleic acid samples from a subject, sequencing target regions in the samples to obtain corresponding sequences and comparing the sequences to identify patient-specific genetic alterations. WO 2014/151117 does not teach the claimed evaluation of sequencing results by sequencing parameters, or the claimed combining of sequencing results into “union sequencing” results. However, WO 2020/221783 teaches preparing two or more biological samples for nucleic acid sequencing, sequencing the biological samples to yield initial sequencing results, evaluating the initial sequencing results by analyzing sequencing parameters, and combining the initial sequencing results based on the sequencing-parameter analysis to yield union sequencing results; under the broadest reasonable interpretation, the claimed “union sequencing” results encompass a merged or consensus resulting output derived from combined sequencing results. WO 2020/221783 further teaches scoring predicted immunogenicity of neoepitopes based on the sequencing data. Additionally, US 12,545,963 teaches a laboratory execution system having centralized data management and analytics results management that synthesize raw test data.
Regarding claims 3-8, WO 2020/221783 teaches the sample limitations recited in these claims. In particular, WO 2020/221783 discloses that each biological sample may independently be a biopsy sample including an excisional biopsy, liquid biopsy, incisional biopsy, needle biopsy, punch biopsy, or shave biopsy; that at least two biological samples may be from different regions of the body; that at least two biological samples may be from different regions of a tumor; that at least one biological sample may be from a primary tumor; that at least one biological sample may be from a secondary tumor; and that at least two biological samples may be collected at different occasions separated by at least about 1 day. WO 2014/151117 provides the sequencing and comparison framework for multiple samples, and US 12,545,963 provides the automated laboratory environment.
Regarding claims 9–12, WO 2020/221783 teaches evaluating sequencing results using sequencing parameters including number of sequence reads, number of sequencing variants, tumor purity, sequencing depth, number of protein-modifying sequencing variants, RNA confirmation rate, RNA quality, number of long identified neoantigen peptides, number of short identified neoantigen peptides, and predicted immunogenicity of a neoantigen peptide. WO 2020/221783 further teaches comparing union sequencing (under BRI) parameters to initial sequencing parameters to determine whether results should be combined or whether a representative biological sample should be selected. WO 2014/151117 provides the underlying sequencing-and-comparison framework, and US 12,545,963 teaches automated synthesis and management of raw test data.
Regarding claims 13–19, WO 2020/221783 teaches that the nucleic acid sequencing may be of RNA, DNA, or a combination thereof; that sequencing may be performed by whole exome sequencing, whole genome sequencing, RNA sequencing, single cell sequencing, targeted panel sequencing, and combinations thereof; that at least two different sequencing techniques may be used; that different biological samples may be sequenced by different sequencing techniques; and that subsequent sequencing of a biological sample or representative biological sample may be performed using the same or different sequencing techniques. WO 2014/151117 provides the sequencing-and-comparison backbone, and US 12,545,963 provides the automated laboratory environment.
Regarding claims 20–22, WO 2020/221783 teaches that the one or more neoantigens may be peptides selected from long peptides, short peptides, and combinations thereof; that a neoantigen vaccine may be generated comprising or encoding selected neoantigens; and that the neoantigen vaccine may be administered to the subject in need thereof. WO 2014/151117 provides the sequencing-derived patient-specific alteration identification from which neoantigen candidates are obtained, and US 12,545,963 provides the automated laboratory workflow.
There is a sufficient rationale to combine the references because they address complementary parts of a predictable personalized cancer-analysis workflow. WO 2014/151117 provides patient-specific sequencing and alteration identification; WO 2020/221783 provides downstream sequencing-parameter evaluation and neoepitope prioritization; and US 12,545,963 provides the automated laboratory data-management framework for implementing and processing the workflow. Combining these teachings would have predictably improved the efficiency and manageability of sequencing-based neoantigen selection and downstream vaccine or cellular therapy preparation.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to one of ordinary skill art to combine the tumor/genomic sequencing and comparison teachings of WO 2014/151117 with the neoepitope-selection and sequencing-parameter evaluation teachings of WO 2020/221783, and to implement the resulting workflow in the automated laboratory environment of US 12,545,963, in order to improve sequencing analysis efficiency and identify clinically relevant neoepitopes for downstream vaccine or cellular therapy use.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Gary Benzion whose telephone number is (571)272-0782. The examiner can normally be reached M-F, 9am to 5pm.
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GARY BENZION, Ph.D.
Supervisory Patent Examiner
Art Unit 1681
/GARY BENZION/ Supervisory Patent Examiner, Art Unit 1681
Prosecution Insights