DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Applicant's amendments and remarks, filed, 12/09/2025, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1, 2, 5, 6, 8, 9, 12, 14, 15, 18 are under examination.
Claims 3, 4, 7, 10, 11, 13, 16, 17, 19, 20 are cancelled.
Priority
This application is a continuation of U.S. Patent Application Serial No. 16/691,480, filed November 21, 2019, which is a continuation of U.S. Patent Application Serial No. 14/554,715, filed November 26, 2014, which is a continuation of U.S. Patent Application Serial No. 13/164,499, filed June 20, 2011, which claims priority to U.S. Provisional Application Serial No. 61/356,501 filed June 18, 2010.
After further consideration of the claim amendments and applicant’s arguments regarding priority to ‘499, the arguments are persuasive. Accordingly, the effective filing date for the instant application is 06/20/2011.
Withdrawn Rejections
The rejection of claims 7 and 13 under 35 U.S.C. 102(b) as being anticipated by or, in the alternative, under 35 U.S.C. 103(a) as being obvious over Ossovskaya et al. (US 20080262062; filed Nov. 7, 2007) is withdrawn in view of applicant’s amendments (which cancelled these claims).
The rejection of claims 1-6, 8-12, 14-20 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Abkevich et al. (WO/2011/160063; Pub. Date: 12/22/2011) is withdrawn in view of applicant’s arguments and the new effective priority date of the instant application (June 20, 2011).
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, 2, 5, 6, 8, 9, 12, 14, 15, 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and ‘as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355).
Guidance Step 1: Under the broadest reasonable interpretation, the claimed invention (claims 1, 8, 14 being representative) is directed to methods (and a system) of detecting homologous recombination deficiency in a cancer cell. Therefore, the claims fall into one of the four statutory categories. [Step 1: YES]
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. Regarding claim(s) 13, the following steps encompass an abstract idea:
(a) detecting determining, in at least one pair of human chromosomes in the cancer cell, a total number of LOH regions in at least one pair of human chromosomes of said cancer cell that are longer than 15 megabases a first length but shorter than the length of the whole chromosome containing the LOH region, wherein said the at least one pair of human chromosomes is not a human X/Y sex chromosome pair, wherein said first length is about 15 or more megabases…; (claims 1, 8, 14)
(b) detecting HRD in the cancer cell when the total number of LOH regions is equal to or greater than 9 (claim 1)
(b) detecting the absence of HRD in the cancer cell when the total number of LOH regions is less than 9 (claims 8, 14)
Mental Processes
Regarding claim(s) 1, 8, 14, the claimed detecting steps are not limited to any particular acts or operations. Accordingly, under the BRI, the claimed determining encompasses observations and/or analysis. Moreover, a review of the specification describes computational and/or algorithmic methods for determining LOH regions [0019-0021, 0062]. As such, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data reception and analysis, which may be performed in the human mind via normal processes of observation and evaluation. For these reasons, the above step falls within the mental process groupings of abstract ideas. See MPEP 2106.04(a)(2), subsection III. [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
Having made that determination, under the 2019 Guidance, the examiner next determines whether there are additional elements beyond the recited abstract idea(s) that integrate them into a practical application.
In this case, the additional steps/elements that are not part of the abstract idea are as follows:
a sample analyzer configured to produce a plurality of signals about genomic DNA… (claim 14);
a computer sub-system programmed to detect… (claim 14)
With regards to the “sample analyzer” configured to produce signals, this is recited at a high level of generality and is merely used as a tool to obtain data for use by the abstract idea. Therefore, the above step amounts to no more insignificant extra-solution activity. See MPEP 2106.05(f). Regarding the computer sub-system, this feature is generically recited and reads on a computer used as a tool to obtain information or perform the abstract idea. Moreover, applicant is reminded that “generic computer components such as a computer and database do not satisfy the inventive concept requirement.” See MPEP 2106.05(f) and 2106.05(h). Even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO]. For a list of considerations when evaluating whether additional elements integrate a judicial exception into a practical application see MPEP 2106.04(d)(1) lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05.
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. A review of the specification does not teach that there is anything inventive with regards to the claimed “analyzer” or “computer sub-system”. Moreover, Nannya et al. (Cancer Res, 2005; 65; pp. 6071-79) teach conventional tools (e.g. genomic arrays) for detecting LOH in regions associated with at least 15 chromosomes that are shorter than the whole chromosome and covering a plurality of different lengths ranging from 5kb up to 8.7 megabases [Table 1, Figure 3]. Abkevich et al. (WO/2011/160063; Pub. Date: 12/22/2011) teaches routine and conventional methods for determining LOH signatures in at least one pair of human chromosomes [pages 5, 22, and 35, and ref. claim 2]. With regards to the claimed computer sub-system, this is nothing more than a generically recited, routine and conventional element, and the courts have explained that the use of generic computer elements do not alone transform an otherwise abstract idea into patent-eligible subject matter. See DDR Holdings (Fed. Cir. 2014). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
Dependent claims 2, 5, 6, 9, 12, 15, 18 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. In particular, claims 2, 5, 6, 9, 12, 15, 18 further limit the nature of the data used by the abstract idea and data is not patentable. Therefore, these claims also encompass one or more abstract ideas and are not patent eligible for reasons discussed above (Step 2A, prong 1). Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Response to Arguments
Applicant’s arguments, filed 12/09/2025, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claims are no patent eligible in view of the amendments (which have removed the correlating, calculating, and determining steps). In response, the examiner maintains that the claims are still directed to an abstract idea for reasons set forth above (Step 2A, prong 1 analysis). In addition, the instant claims do not recite an integration of the abstract idea into a practical application for reasons set forth above (Step 2A, prong 1 and Step 2B analysis). Accordingly, the abstract idea is implemented on generic components that are recited at a high level of generality and are well-understood, routine, and conventional, and there is nothing in the specification to support a position that the claimed invention is directed to an improvement in the technology or a particular machine (as in Enfish). See MPEP 2106.04(d)(1) and MPEP 2106.05(a). For at least these reasons, the examiner maintains that he has properly applied the two-step analysis as explained in MPEP 2106.04(a)(2), subsection III, and that the claims are not patent eligible. In the interest of advancing prosecution and overcoming the rejection set forth above, the examiner suggests reviewing the allowed claims for related application 16/691,480 (now US 11,174519).
Claim rejections - 35 USC § 112, 1st Paragraph
The following is a quotation of 35 U.S.C. 112(a):
IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
This is a written description rejection.
Claims 1, 2, 5, 6, 8, 9, 12, 14, 15, 18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The written description requirement is separate and distinct from the enablement requirement. The specification must: (1) describe the claimed invention in a manner understandable to a person of ordinary skill in the art, and (2) show that the inventor actually invented the claimed subject matter. In this case, the following limitations lack sufficient written description:
(a) detecting determining, in at least one pair of human chromosomes in the cancer cell, a total number of LOH regions in at least one pair of human chromosomes of said cancer cell that are longer than 15 megabases a first length but shorter than the length of the whole chromosome containing the LOH region, wherein said the at least one pair of human chromosomes is not a human X/Y sex chromosome pair, wherein said first length is about 15 or more megabases…; (claims 1, 8, 14)
(b) detecting HRD in the cancer cell when the total number of LOH regions is equal to or greater than 9 (claim 1)
(b) detecting the absence of HRD in the cancer cell when the total number of LOH regions is less than 9 (claims 8, 14)
With regards to the claimed “detecting”, these limitations are generically recited any not limited to any particular computational operations or genetic markers, i.e. the claims generically encompass any and every means for performing the claimed functions. A review of the specification teaches a limited embodiment wherein an “algorithm” is implemented as a computer program and used to reconstruct an LOH signature for a specific set of tumors from patients with ovarian cancer [Example 1]. However, this is not commensurate in scope with what is being claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. In other words, the claimed method is essentially using a black box algorithm for achieving the claimed function. As such, the instant specification fails to disclose the requisite computational steps and/or program code that must be practiced in order to realize the subsequently recited functionality.
Furthermore, one of ordinary skill in the art would recognize that algorithms for predicting HRD in cells are not trivial. In particular, the post-filing art of Telli et al. (Clin Cancer Res; 2016; 22(15), pp.3764-73) teaches computational methods for detecting HRD. In particular, unlike the instant claims, Telli teaches analyzing DNA using a NGS–based assay to generate specific genome-wide SNP profiles and using a well-defined model that is validated and based on a plurality of different parameters (e.g. LOH, TAI, LST) [See entire]. In other words, there is no universal model (and associated threshold value) for detecting HRD as the model choice and parameters vary upon the nature of the cancer and therapy being used with the patient. For the reasons discussed above, the specification does not provide a sufficient disclosure of the requisite information such that one of skill in the art would have been aware that applicants were actually in possession of such “products” at the time of invention.
Response to Arguments
Applicant’s arguments, filed 12/09/2025, have been fully considered but are moot in view of the modified rejection (which is necessitated by applicant’s amendments).
Claim rejections - 35 USC § 112, 2nd Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 2, 5, 6, 8, 9, 12, 14, 15, 18 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claims 1, 8, 14 are also rejected due to said dependency.
Claims 1, 8, 14 recite “detecting determining, in at least one pair of human chromosomes in the cancer cell, a total number of LOH regions in at least one pair of human chromosomes of said cancer cell that are longer than 15 megabases a first length but shorter than the length of the whole chromosome containing the LOH region, wherein said the at least one pair of human chromosomes is not a human X/Y sex chromosome pair…”. Such generic functional claim language amounts to descriptions of problems to be solved and covers all means or methods of performing the claimed function. A review of the specification does not describe, to any appreciable extent, any particular algorithms, equations, or prose equivalent that correspond to the claimed function. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment.
Nonstatutory 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. See 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);and, 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) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent is shown to be commonly owned with this application. See 37 CFR 1.130(b).
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 1, 2, 5, 6, 8, 9, 12, 14, 15, 18 is/are provisionally rejected under the judicially created doctrine of obviousness-type double patenting as being unpatentable over claims 1-36 of US Patent 9,388,472. Although the conflicting claims are not identical, they are not patentably distinct from each for the following reasons:
In the present case, reference claim 1 of the ‘472 patent recites all the limitations of those required by instant claim 1 plus additional limitations (e.g. assaying, providing, and determining steps). An obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but an examined application claim is not patentably distinct from the reference claims because the examined claim is either anticipated by, or would have been obvious over, the reference claims. 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). Therefore, above instant claim(s) is/are anticipated by the narrower reference claims of the issued patent
Claims 1, 2, 5, 6, 8, 9, 12, 14, 15, 18 is/are provisionally rejected under the judicially created doctrine of obviousness-type double patenting as being unpatentable over claims 1-29 of copending application 19/088442. Although the conflicting claims are not identical, they are not patentably distinct from each for the following reasons:
In the present case, reference claim 1 of the ‘442 application patent recites all the limitations of those required by instant claim 1 plus additional limitations (e.g. assaying, providing, and determining steps). An obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but an examined application claim is not patentably distinct from the reference claims because the examined claim is either anticipated by, or would have been obvious over, the reference claims. 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). Therefore, above instant claim(s) is/are anticipated by the narrower reference claims of the issued patent
Response to Arguments
Applicant’s arguments, filed 12/09/2025, have been fully considered but are not persuasive as applicant is not provided any specific reasoning that would serve to challenge the examiner’s position or any terminal disclaimers. Accordingly, the rejections are maintained for the reasons of record.
Conclusion
No claims are allowed.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619