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 .
This action is in response to papers filed 2/11/2025.
Applicant’s election of BRAC1 in the reply filed on 6/13/2023 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 1-6, 8-9, 11-12, 20-23 are pending. Claims 7, 10, 13-19 have been cancelled.
The following rejections are maintained with response to arguments following.
This action is FINAL.
Withdrawn objections and rejections
The obviousness double patenting rejection over US Application No. 17381272 is withdrawn based upon cancellation of US Application No. 17381272.
Claim Rejections - 35 USC § 103
7. 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 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.
8. The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
9. This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
10. Claim(s) 1-6,8-9,11,12,20-23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Popova et al. (Cancer Research Vol 72 Nov 1, 2012 cited on IDS).
With regard to claim 1, Popova et al. teaches a method of sequencing genomic DNA from a tumor (p. 5458 2nd paragraph). Popova et al. teaches detection of LST that is at least 3 megabases (Figure 2). Although Popova et al. does not teach specification at least 11 LST detection and tumor deficiency in the DNA HR pathway, Popova et al. suggests that a high level of LST may be a marker of HR pathway deficiency (p. 560 3rd parpaghra). Popova et al. further teaches segments that span 6 to 11 MB (p. 5457 2nd column). Therefore it would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date use the 11 MB LSTs as a determination for tumor deficiency as Popova suggests that these high levels may be a marker of HR pathway deficiency.
With regard to claim 2-3, Popova et al. teaches detection of activation of BRCA1 and BRCA2 (figure 2, 3)
With regard to claim 4, Popova et al. teaches that the cancer is breast cancer (p. 5459 2nd column 3rd paragraph).
With regard to claim 5, Popova et al. teaches samples that have overexpression of HER2 (p. 65455 2nd column).
With regard to claim 6, Popova et al. teaches a method wherein the number of breakpoints is quantified by detecting copy number variations (p. 5457 2nd column and figure 2).
With regard to claim 8, Popova et al. teaches evaluating the ploidy of each subject (p. 5458 1st paragraph).
With regard to claim 9, Popova et al. teaches methods of evaluating ploidy by SNP array (p. 5458 2nd paragraph).
With regard to claim 11, Popova et al. teaches a method of sequencing genomic DNA from a tumor (p. 5458 2nd paragraph). Popova et al. teaches evaluating the ploidy of each subject (p. 5458 1st paragraph).Popova et al. teaches detection of LST that is at least 3 megabases (Figure 2). Although Popova et al. does not teach specification at least 11 LST detection and tumor deficiency in the DNA HR pathway, Popova et al. suggests that a high level of LST may be a marker of HR pathway deficiency (p. 560 3rd parpaghra). Popova et al. further teaches segments that span 6 to 11 MB (p. 5457 2nd column). Therefore it would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date use the 11 MB LSTs as a determination for tumor deficiency as Popova suggests that these high levels may be a marker of HR pathway deficiency.
With regard to claim 12, Popova et al. teaches methods of evaluating ploidy by SNP array (p. 5458 2nd paragraph).
With regard to claims 20-21, Popova et al. teaches detection of LST that is at least 3 megabases (Figure 2). Popova et al. further teaches segments that span 6 to 11 MB (p. 5457 2nd column 5460 1st column 1st paragraph).
With regard to claims 22-23, the limitation of “ providing a written or electronic report” appears to be an abstract limitation that would encompass any written information. As Popova provides figures these would be encompassed by a written report.
Response to arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguments following. The reply asserts that Popova does not teach or suggest tumor deficiency in the DNA HR pathway when at least 11 LSTs of at least 3 megabases per genome are detected (p. 5-6). The reply asserts that the recitation of 11 MB LSTs is not the same as 11 LSTs of at least 3 MBs (p. 6). These arguments have been reviewed but have not been found persuasive. Although Popova et al. does not teach specification at least 11 LST detection and tumor deficiency in the DNA HR pathway, Popova et al. suggests that a high level of LST may be a marker of HR pathway deficiency (p. 560 3rd parpaghra). Popova et al. further teaches segments that span 6 to 11 MB (p. 5457 2nd column). Therefore it would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date use the 11 MB LSTs as a determination for tumor deficiency as Popova suggests that these high levels may be a marker of HR pathway deficiency. Popova teaches genomic instability in HR pathway deficiency based upon the instability of BRCA1 and 2. As such Popova suggests the use of LST transitions of at least 3 megabases in the same pathway, it would be obvious to one of ordinary skill in the art to screen all segments in this region which would be at least 11 LSTs.
Double Patenting
12. 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 §§ 706.02(l)(1) - 706.02(l)(3) 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.
14. Claims 1-6, 11-12, 20-23 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 11149316. Although the conflicting claims are not identical, they are not patentably distinct from each other. Each set of claims encompass methods of detecting tumor deficiency based upon rearrangements of megabases in the homologous recombination pathway and treatment. The claims differ as the patent requires “at least 6”, however, the instant application “at least 3” would be encompassed in the scope. Furthermore, the claims are drawn not only to treating but predicting tumor deficiency. However, the steps of the instant claims and the patent are identical in the analysis of quantifying the number of rearrangements.
Response to arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguetmsn following. The reply asserts the reference applications/patents are drawn to methods of treatment (p. 8). Although the patent is drawn to treating, the method steps of the patent encompasses the steps of predicting tumor deficiency which is claimed by the instant application. The reply asserts that the examiner has not determined whether the grant of a second paten would give rise to an unjustified expression of rights and the reply asserts as the claims do not recite the step of treatment that this would not unjustly extend (p. 7-8). This argument has been reviewed but is not found persuasive. In particular, MPEP 804 states Nonstatutory double patenting includes rejections based on anticipation, a one-way determination of “obviousness,” or a two-way determination of “obviousness.” It is important to note that the “obviousness” analysis for “obviousness-type” double-patenting is “similar to, but not necessarily the same as, that undertaken under 35 U.S.C. 103.” In re Braat, 937 F.2d 589, 592-93, 19 USPQ2d 1289, 1292 (Fed. Cir. 1991) (citing In re Longi, 759 F.2d 887, 892 n.4, 225 USPQ 645, 648 n.4 (Fed. Cir. 1985)); Geneva Pharmaceuticals, 349 F.3d 1373, 1378 n.1, 68 USPQ2d 1865, 1869 n.1 (Fed. Cir. 2003). In addition, nonstatutory double patenting also includes rejections based on the equitable principle against permitting an unjustified timewise extension of patent rights. See In re Schneller, 397 F.2d 350, 158 USPQ 210 (CCPA 1968); see also subsection II.B.6, below. Herein the analysis is a one way determination as the Patent includes all the steps of the pending claims. For one way analysis the fact that the instant claims do not recite a step of treatment is not relevant as the US patent includes all pending steps (e.g. one way analysis).
Claims 1-6, 11-12, 20-23 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11091808.
Although the conflicting claims are not identical, they are not patentably distinct from each other. Each set of claims encompass methods detecting based upon rearrangements of at least 3 megabases of LSTs. Furthermore, the claims are drawn not only to treating but predicting tumor deficiency. However, the steps of the instant claims and the patent are identical in the analysis of quantifying the number of rearrangements.
Response to arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguetmsn following. The reply asserts the reference applications/patents are drawn to methods of treatment (p. 8). Although the patent is drawn to treating, the method steps of the patent encompasses the steps of predicting tumor deficiency which is claimed by the instant application. The reply asserts that the examiner has not determined whether the grant of a second paten would give rise to an unjustified expression of rights and the reply asserts as the claims do not recite the step of treatment that this would not unjustly extend (p. 7-8). This argument has been reviewed but is not found persuasive. In particular, MPEP 804 states Nonstatutory double patenting includes rejections based on anticipation, a one-way determination of “obviousness,” or a two-way determination of “obviousness.” It is important to note that the “obviousness” analysis for “obviousness-type” double-patenting is “similar to, but not necessarily the same as, that undertaken under 35 U.S.C. 103.” In re Braat, 937 F.2d 589, 592-93, 19 USPQ2d 1289, 1292 (Fed. Cir. 1991) (citing In re Longi, 759 F.2d 887, 892 n.4, 225 USPQ 645, 648 n.4 (Fed. Cir. 1985)); Geneva Pharmaceuticals, 349 F.3d 1373, 1378 n.1, 68 USPQ2d 1865, 1869 n.1 (Fed. Cir. 2003). In addition, nonstatutory double patenting also includes rejections based on the equitable principle against permitting an unjustified timewise extension of patent rights. See In re Schneller, 397 F.2d 350, 158 USPQ 210 (CCPA 1968); see also subsection II.B.6, below. Herein the analysis is a one way determination as the Patent includes all the steps of the pending claims. For one way analysis the fact that the instant claims do not recite a step of treatment is not relevant as the US patent includes all pending steps (e.g. one way analysis).
Conclusion
No claims are allowed.
15. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu Cheng (Winston) Shen can be reached on 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KATHERINE D SALMON/Primary Examiner, Art Unit 1682
