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 Claim(s)
Claims 1-21 have been examined. Claim 1has been amended..
Priority
This application is is a continuation of US. Patent Application No 17822058, filed on 08/24/2022, wwhich is a continuation of US. Patent Application No.17/818,944 filed on 08/10/2022, which is a continuation of US. Patent Application No. 17/699,968 filed on 03/21/2022, which is a continuation of US Patent No. 17/462,906 filed on 08/31/2021, which is a continuation of US. Patent No. 17/000,010 filed on08/21/2020, which is a continuation of US. Patent No. 15/431,395 filed on 02/13/2017, which is a continuation of Internation Patent Application No. PCT/US2015/067717 12/28/2015 filed 12/28/2015, which claims the benefit of US. Provisional Application No.62/098,426 filed 12/31/2014 and US Provisional Application No. 62/155,763 filed on 05/01/2015
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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 17000010. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the database to identify tumor genomic testing data comprising somatic alterations and therapeutic interventions administered to each of the subjects. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the use of database to infer efficacy of the therapeutic interventions in subjects with a tumor genomic profile.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 17822058. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the database to include, for each of a plurality of subject having tumor genomic testing data including somatic alterations and therapeutic interventions administered to each of the subjects at one or more times and efficacy of the therapeutic interventions. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the use of database to infer efficacy of the therapeutic interventions in subjects with a tumor genomic profile.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 17462906. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the database to include, for each of a plurality of subject having tumor genomic testing data including somatic alterations and therapeutic interventions administered to each of the subjects at one or more times and efficacy of the therapeutic interventions. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the use of database to infer efficacy of the therapeutic interventions in subjects with a tumor genomic profile.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 15431395. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the database to identify tumor genomic testing data comprising somatic alterations and therapeutic interventions administered to each of the subjects. Although the claims at issue are not identical, they are not patentably distinct from each other because both claims recite the use of database to infer efficacy of the therapeutic interventions in subjects with a tumor genomic profile.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Allowable Subject Matter Over the Prior Art
The primary reason for indicating allowability over the prior art is the inclusions of the following limitations in the combination as recited.
Claim 1 is directed towards a method of developing a disease cell heterogeneity profile for a cancer in a patient, comprising:
(a) receiving sequence information generated from a plurality of nucleic acids from a bodily fluid sample from the patient, wherein the plurality of the nucleic acids comprise cell-free deoxyribonucleic acid (cfDNA) molecules, wherein the cfDNA was tagged or tracked with molecular barcodes to permit subsequent identification of a particular polynucleotide and, wherein the molecular barcodes track back to single original cell-free nucleic acid molecules;
(b) determining and quantifying mutant allele frequencies (MAF) based on analyzing the sequence information;
(c) developing a disease cell heterogeneity profile for the patient based on the determination and quantification of step (b); and
(d) inferring efficacy of a given therapeutic intervention, predicting tumor genomic evolution and/or acquisition of resistance mechanisms in the patient by applying a machine learning algorithm to the disease cell heterogeneity profile, the machine learning algorithm a feature vector comprising the patient’s somatic alterations and a temporal change metric for each alteration, the temporal change metric equal to a difference in relative variant frequency of the alteration between at least a first and a second cfDNA biopsy of the patient, the support vector machine trained by using data associated with one or more therapeutic interventions and data associated with efficacy of the one or more therapeutic interventions from a database.
For claim rejection under 35USC 101, the current invention recites “a machine learning algorithm comprising a support vector machine to a feature vector comprising the patient’s somatic alterations and a temporal change metric for each alteration..”. As described in MPEP2106.04-.07, the combination of recited additional elements in the recited claims is patent eligible because the claims as a whole integrate an abstract idea into practical application under Prong Two of Step 2A of the Alice/Mayo Test as described in MPEP2106.04-07. The claims are eligible because it is not directed to an abstract idea or any other judicial exception.
The closest prior art relates to Diehn, Maximillan (WO2014151117A1 hereinafter Diehn, Maximillan) in view of Lloyd et al. (WO2015069827A2 hereinafter Lloyd). Diehn, Maximillan disclose methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation. Lloyd discloses personalized cancer therapy using analysis of pathology slides to target regions in a single sample that interrogates the feature data of a relatively large number of cells. The disclosure describes pathology case review tools of the future which include analysis, visualization and prediction modeling to provide novel information to the pathologist for the diagnosis of disease. This disclosure further describes a user interface to assist the physicians that make that diagnosis, pathologists. Complex computer learning algorithms will combine and mine these data sets to recommend optimal treatment strategies.
The foreign reference, WO2018213498A1, discloses systems and methods to detect somatic or germline variants from cell-free DNA (cfDNA), to receiving sequencing information from cfDNA from said subject, said sequencing information comprising cfDNA sequencing reads from said plurality of genomic loci.
However, the combined art and foreign reference fail to teach “inferring efficacy of a given therapeutic intervention, predicting tumor genomic evolution and/or acquisition of resistance mechanisms in the patient by applying a machine learning algorithm to the disease cell heterogeneity profile, the machine learning algorithm a feature vector comprising the patient’s somatic alterations and a temporal change metric for each alteration, the temporal change metric equal to a difference in relative variant frequency of the alteration between at least a first and a second cfDNA biopsy of the patient, the support vector machine trained by using data associated with one or more therapeutic interventions and data associated with efficacy of the one or more therapeutic interventions from a database.”
Claims 1-21 would be allowable if rewritten to overcome the rejection(s) under Double Patenting, as set forth in this Office action and to include all of the limitations of the base claim and any intervening claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
US 20130136799, May 30, 2013, Faham, Monitoring Health and Disease Status Using Clonotype Profile.
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.
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/HIEP V NGUYEN/Primary Examiner, Art Unit 3686
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