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 .
Remarks
In response to communications sent March 12, 2024 claim(s) 21-29 are pending in this application; of these claim 21 is in independent form.
Response to Amendment
The preliminary amendments to the specification and the claims, filed March 12, 2024, are acknowledged and have been entered into the record.
Drawings
The drawings are objected to because the “TDP Classification” legend and graph of Figure 1D depicts shades of grey that are indistinguishable from each other. The Examiner recommends using shading patterns such as hatched lines and various angles or dots at various densities in order to further distinguish between different shades of the legend and graph. See the file wrapper of the parent application 16/238,764, which includes a clearer drawing filed on September 8, 2023 in the parent application. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The abstract of the disclosure is objected to because the one short sentence provides inadequate description. Correction is required. See MPEP § 608.01(b).
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
See, for example, the last line of page 30, lines 9 and 30 of page 31, line 12 of page 34, and line 5 of page 35.
The disclosure is objected to because of the following informalities: Page 4 line 20 mentions the color blue, but the drawings are in black and white. Additionally, page 5 line 18 mentions the colors red and blue. The Examiner suggests amending the specification to identify the portions referred to a “blue” or “red” using a descriptor that corresponds to black and white drawings.
Appropriate correction is required.
Information Disclosure Statement
The Information Disclosure Statement(s) is/are acknowledged and the references contained therein have been considered by the Examiner. This includes the Information Disclosure Statements(s) filed on: June 7, 2024
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Objections
Claims 21-29 are objected to because of the following informalities: Claim 21 recites ERRB2, which appears to be a typographical error for the true human gene ERBB2. Claims 22-29 are objected to because they depend from the independent claim 21. Appropriate correction is required.
Claims 21-29 are objected to because of the following informalities: Claim 21 recites MYC1, which appears to be a typographical error for the true human gene MYC. See Applicant’s specification at page 17 which describes “MYC1” as being the gene with GeneID 4609. The Examiner interprets that the gene with that GeneID is the MYC gene. Claims 22-29 are objected to because they depend from the independent claim 21. Appropriate correction is required.
Claim Interpretation
The broadest reasonable interpretation of “and/or” is the disjunction “or”. The phrase “and/or” appears in the independent claim 21, and its limitations are a part of the dependent claims.
Claim Analysis - 35 USC § 101
Claim 21 recites a mental process of “identification…”. Nevertheless, the identification step is integrated into a practical application because the administration step applies to “the subject”; the phrase “the subject” has antecedent basis in the identification step for a subject. Hence the practical application is applied to the identified subjects, thus integrating the identification with the treatment. The treatment is a particular treatment because it specifies two particular classes of chemotherapy drugs.
Claims 21-29 recite further limitations to the mental process and abstract ideas without removing the integration into a practical and particular treatment.
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.
Claim(s) 21-29 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Menghi, Francesca, et al. "The tandem duplicator phenotype as a distinct genomic configuration in cancer." Proceedings of the National Academy of Sciences 113.17 (2016): E2373-E2382. The reference shall hereinafter be referred to as “Menghi.”
(This reference was cited on Applicant’s Information Disclosure Statement and a copy was provided in the file wrapper of the parent application 16/238,764.)
As to claim 21, Menghi teaches a method, comprising:
(a) identifying a subject as a candidate for a therapy (Menghi 2016, page E2379 lines 23-47: a discovery to assign subjects as candidates for cisplatin therapy based on at least one subtype of the tumor sample) that targets a tumor comprising tandem duplications in PTEN, RB1, NF1, ERRB2, MYC1, ESR1, MDM2 and/or lncRNA MALAT1 (these elements are claimed in the alternative and only some need to be mapped) based on a tandem duplicator phenotype (TDP) subtype of the tumor (Menghi 2016, page E2376-E2377 column 2 line 8 column 2 line 9: identifying a subject as having a particular tandem duplication in ERBB2, suggesting that the subject is a candidate for anti-cancer treatment); and
(b) administering to the subject a therapy that comprises a platinum-based agent (Menghi 2016, page E2379 lines 23-47: a discovery to assign subjects as candidates for cisplatin therapy based on at least one subtype of the tumor sample) and/or an alkylating agent (the broadest reasonable interpretation of “and/or” is “or”; see Nik-Zainal Para [0027]: administering a therapy based on the signatures 1 or 3 of the sample, such as platinum-based therapy or PARP inhibitors).
As to claim 22, Menghi teaches the method of claim 21, wherein the identifying comprises:
(i) calculating a TDP score (Menghi 2016, page E2373 last paragraph to E2374 first paragraph: the reference teaches the precise equation for determining tandem duplication score) for the genome of the tumor (Menghi 2016, page E2374 lines 10-34: obtained from subjects having a human genome),
wherein the TDP score is calculated using the following equation:
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wherein tandem duplication (TD) is total number of tandem duplications in the tumor, Obsi is observed number of tandem duplications for each chromosome i in the genome, Expi is expected number of tandem duplications for each chromosome i in the genome, and k is 0.71 (Menghi 2016, page E2373 last paragraph to E2374 first paragraph: the reference teaches the precise equation for determining tandem duplication score);
(ii) measuring a length distribution of tandem duplications in the tumor with a TDP score is above a threshold value of zero (0) (Menghi 2016, page E2374 lines 10-34: applying a threshold of zero); and
(iii) assigning to the tumor (Menghi 2016, page E2374 lines 10-34: assigning tumor samples to at least one of three trimodal categories based on the score derived from the length distributions; by broadest reasonable interpretation, the assignment is to the first subtype) the TDP subtype (see Applicant’s Figure 1B, which indicates various subtypes that are: 1-and-3, 1-and-3, and 2-and-3 combinations of subtypes in addition to just-1, just-2, and just-3) based on the length distribution of the tandem duplications (Menghi 2016, page E2374 lines 10-34: subtypes are derived from the length distributions).
As to claim 23, Menghi teaches the method of claim 21, wherein the TDP subtype is selected from the group consisting of: Group 1 TDP subtype, Group 2 TDP subtype, Group 3 TDP subtype (Menghi 2016, page E2374 lines 10-34: assigning tumor samples to at least one of three trimodal categories based on the score derived from the length distributions), Group 1/2mix TDP subtype, Group 1/3mix TDP subtype, and Group 2/3mix TDP subtype (the six subtypes of the claim are interpreted to involve using permutations of subtypes is consistent with Applicant’s Figure 1B, which indicates 1-and-3, 1-and-3, and 2-and-3 combinations of subtypes in addition to just-1, just-2, and just-3; the Examiner argues that a score selected from at least one of three subtypes has the property that the one selected score is inherently selected from among combinations of “one or two” subtypes selected from among the three subtypes, including 6 permutations).
As to claim 24, Menghi teaches the method of claim 23, wherein the Group 1 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb (Menghi 2016, page E2375 lines 12-25: TD span distribution modes at ∼10 kb).
As to claim 25, Menghi teaches the method of claim 23, wherein the Group 2 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 231 kb (Menghi 2016, page E2375 lines 12-25: TD span distribution modes at ∼250 kb).
As to claim 26, Menghi teaches the method of claim 23, wherein the Group 3 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 1.7 Mb (Menghi 2016, page E2375 lines 12-25: 1,189.7 kb for non-TDPs).
As to claim 27, Menghi teaches the method of claim 23, wherein the Group 1/2mix TDP subtype (the six subtypes of the claim are interpreted to involve using permutations of subtypes is consistent with Applicant’s Figure 1B, which indicates 1-and-3, 1-and-3, and 2-and-3 combinations of subtypes in addition to just-1, just-2, and just-3; the Examiner argues that a score selected from at least one of three subtypes has the property that the one selected score is inherently selected from among combinations of “one or two” subtypes selected from among the three subtypes, including 6 permutations) is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb (Menghi 2016, page E2375 lines 12-25: TD span distribution modes at ∼10 kb) and tandem duplications having a length of about 231 kb (Menghi 2016, page E2375 lines 12-25: TD span distribution modes at ∼250 kb).
As to claim 28, Menghi teaches the method of claim 23, wherein the Group 1/3mix TDP subtype (the six subtypes of the claim are interpreted to involve using permutations of subtypes is consistent with Applicant’s Figure 1B, which indicates 1-and-3, 1-and-3, and 2-and-3 combinations of subtypes in addition to just-1, just-2, and just-3; the Examiner argues that a score selected from at least one of three subtypes has the property that the one selected score is inherently selected from among combinations of “one or two” subtypes selected from among the three subtypes, including 6 permutations) is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb (Menghi 2016, page E2375 lines 12-25: TD span distribution modes at ∼10 kb) and tandem duplications having a length of about 1.7 Mb (Menghi 2016, page E2375 lines 12-25: 1,189.7 kb for non-TDPs).
As to claim 29, Menghi teaches the method of claim 23, wherein the Group 2/3mix TDP subtype (the six subtypes of the claim are interpreted to involve using permutations of subtypes is consistent with Applicant’s Figure 1B, which indicates 1-and-3, 1-and-3, and 2-and-3 combinations of subtypes in addition to just-1, just-2, and just-3; the Examiner argues that a score selected from at least one of three subtypes has the property that the one selected score is inherently selected from among combinations of “one or two” subtypes selected from among the three subtypes, including 6 permutations) is assigned to a tumor sample that comprises tandem duplications having a length of about 231 kb (Menghi 2016, page E2375 lines 12-25: TD span distribution modes at ∼250 kb) and tandem duplications having a length of about 1.7 Mb (Menghi 2016, page E2375 lines 12-25: 1,189.7 kb for non-TDPs).
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.
Claims 21-29 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3 of U.S. Patent No. 11,978,556. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are a genus of the species of the reference patent. For example, the list of genes recited in claim 21 are listed in the alternative and lacks the mathematical elements of claim 1 of the reference patent.
Instant Application 18/602,428
Reference Patent 11,978,556
21. A method, comprising:
(a) identifying a subject as a candidate for a therapy that targets a tumor comprising tandem duplications in PTEN, RB1, NF1, ERRB2, MYC1, ESR1, MDM2 and/or lncRNA MALAT1 based on a tandem duplicator phenotype (TDP) subtype of the tumor; and
(b) administering to the subject a therapy that comprises a platinum-based agent and/or an alkylating agent.
1. A method, comprising:
(a) calculating a tandem duplicator phenotype (TDP) score for a genome of a tumor sample obtained from a subject,
wherein the TDP score is calculated using the following equation:
T
D
P
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c
o
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=
-
∑
i
O
b
s
i
-
E
x
p
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T
D
+
K
wherein tandem duplication (TD) is the total number of tandem duplications in the tumor sample, Obsi is the observed number of tandem duplications for each chromosome i in the genome, Expi is the expected number of tandem duplications for each chromosome i in the genome, and k is 0.71;
(b) measuring a length distribution of tandem duplications in the tumor sample with a TDP score above a threshold value of zero (0);
(c) assigning to the tumor sample one of at least six TDP subtypes based on the length distribution of the tandem duplications, wherein the tumor sample is assigned a Group 1 TDP subtype, a Group 1/2mix TDP subtype, or a Group 1/3mix TDP subtype;
(d) identifying the subject as a candidate for a therapy that targets tumors comprising tandem duplications in PTEN, RB1, and/or NF1 based on the TDP subtype of the tumor sample; and
(e) administering to the subject a therapy that comprises a platinum-based agent and/or an alkylating agent.
22. The method of claim 21, wherein the identifying comprises:
(i) calculating a TDP score for the genome of the tumor, wherein the TDP score is calculated using the following equation:
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=
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O
b
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E
x
p
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T
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+
K
wherein tandem duplication (TD) is total number of tandem duplications in the tumor, Obsi is observed number of tandem duplications for each chromosome i in the genome, Expi is expected number of tandem duplications for each chromosome i in the genome, and k is 0.71;
(ii) measuring a length distribution of tandem duplications in the tumor with a TDP score is above a threshold value of zero (0); and
(iii) assigning to the tumor the TDP subtype based on the length distribution of the tandem duplications.
See claim 1 steps (a), (b), and (c) which correspond to (i), (ii), and (iii).
23. The method of claim 21, wherein the TDP subtype is selected from the group consisting of: Group 1 TDP subtype, Group 2 TDP subtype, Group 3 TDP subtype, Group 1/2mix TDP subtype, Group 1/3mix TDP subtype, and Group 2/3mix TDP subtype.
2. The method of claim 1, wherein the at least six TDP subtypes are selected from the group consisting of: Group 1 TDP subtype, Group 2 TDP subtype, Group 3 TDP subtype, Group 1/2mix TDP subtype, Group 1/3mix TDP subtype, and Group 2/3mix TDP subtype.
24. The method of claim 23, wherein the Group 1 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb.
3. The method of claim 2, wherein the Group 1 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb, the Group 2 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 231 kb, the Group 3 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 1.7 Mb, the Group 1/2mix TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb and tandem duplications having a length of about 231 kb, the Group 1/3mix TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb and tandem duplications having a length of about 1.7 Mb, and the Group 2/3mix TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 231 kb and tandem duplications having a length of about 1.7 Mb.
25. The method of claim 23, wherein the Group 2 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 231 kb.
See claim 3 also.
26. The method of claim 23, wherein the Group 3 TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 1.7 Mb.
See claim 3 also.
27. The method of claim 23, wherein the Group 1/2mix TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb and tandem duplications having a length of about 231 kb.
See claim 3 also.
28. The method of claim 23, wherein the Group 1/3mix TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 11 kb and tandem duplications having a length of about 1.7 Mb.
See claim 3 also.
29. The method of claim 23, wherein the Group 2/3mix TDP subtype is assigned to a tumor sample that comprises tandem duplications having a length of about 231 kb and tandem duplications having a length of about 1.7 Mb.
See claim 3 also.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jesse P Frumkin whose telephone number is (571)270-1849. The examiner can normally be reached Monday - Saturday, 10-5 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSE P FRUMKIN/Primary Examiner, Art Unit 1685 January 5, 2026