DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. 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 Claims
Claims 1-20 are under examination.
Claim Rejections - 35 USC § 102
2. 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)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 3, 5-13, and 15- 20 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Pal et al. (US 2015/0269307).
Regarding claim 1, Pal et al. teach a method that includes obtaining a sample from the patient’s tumor (paragraph [0114]); obtaining, via at least one digital computer programmed with a pathway analysis engine, omics data extracted from the sample (paragraphs [0013] and [0016]); generating, via the at least one digital computer programmed with a pathway analysis engine, predicated pathway activities in the tumor based on the omics data (paragraphs [0022], [0051], [0103], [0116], and [0162]-[0176]); predicting, via the at least one digital computer programmed with a pathway analysis engine, sensitivities of tumor cells to one or more anticancer compounds based on the predicted interrupted pathway activities (paragraphs [0022], [0051], [0103], and [0162]-[0176]); identifying, via at least one digital computer programmed with a pathway analysis engine, at least one anticancer drug predicted to have a successful treatment from the one or more anticancer compounds based on the sensitivities of the tumor cells (paragraphs [0022], [0051], [0103], [0116], and [0162]-[0176]); isolating viable tumor cells associated with the patient’s tumor (paragraph [0114]); validating the at least one anticancer drug as a treatment for the tumor by measuring anticancer activity of the at least one anticancer drug on the isolated viable tumor cells (paragraphs [0051], [0116], [0125]-[0129] and [0131]).
Regarding claim 3, Pal et al teach where the predicted pathway is a down-regulated pathway (paragraph [0124])
Regarding claim 5, Pal et al. teach where the sample comprises RNA or DNA from the tumor (paragraphs [0016] and [0114]).
Regarding claim 6, Pal et al. teach where the sample is a biopsy sample from the tumor (paragraphs [0013], [0016], and [0114]).
Regarding claim 7, Pal et al. teach where the isolated tumor cells comprise cells extracted from the biopsy sample (paragraphs [0013] and [0016]).
Regarding claim 8, Pal et al. teach treating the patient with an anticancer drug (paragraphs [0016] and [0119]).
Regarding claim 9, Pal et al. teach monitoring the patient for indication that the tumor has become resistant to an anticancer drug (paragraph [0051], [0069] and [0161]).
Regarding claim 10, Pal et al. teach repeating the steps if the tumor is resistant to an anticancer drug (paragraphs [0051] and [0069]).
Regarding claim 11, Pal et al. teach validating by measuring anticancer activity in vitro (paragraph [0123]-[0125]).
Regarding claim 12, Pal et al. teach validating by measuring anticancer activity in vivo (paragraph [0119]).
Regarding claim 13, Pal et al. teach engrafting the viable tumor cell in to a mouse (paragraph [0119]).
Regarding claim 15, Pal et al. teach where the step of validating includes validating a range of concentration or duration of an anticancer drug (paragraphs [0069], [0073], and [0125]).
Regarding claim 16, Pal et al. teach where the anticancer activity is a quantified physiological parameter measure by exposing the isolated tumor cell to an anticancer drug (paragraph [125]-[032]).
Regarding claim 17, Pal et al. teach where the quantified physical parameters includes a proliferation or viability parameter (paragraphs [0125]-[0132]).
Regarding claim 18, Pal et al. teach where the omics data includes genomics or proteomics data (paragraphs [0013] and [0016]).
Regarding claim 19, Pal et al. teach where the validation metric is measured from anticancer cancer activity (paragraphs [0119]-[0125])
Regarding claim 20, Pal et al. teach where the validation metric is measured relative to a control group pathway activity (paragraphs [0118]-[0125]).
Claim Rejections - 35 USC § 103
3. 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 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.
4. Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Pal et al. (US 2015/0269307) as applied to claims 1, 3, 5-13, and 15- 20 above, and further in view of Brubaker et al. (“Drug Intervention Response Prediction with PARADIGM (DRIPP) Identifies Drug Resistant Cancer Cell lines and Pathway Mechanisms of Resistance”, Pac. Symp. Biocomput. (2014) pages 125-135).
Pal et al. is applied as above.
Brubaker et al. teach where the predicted pathway activities comprise PARADIGM predicted pathway activities (pages 5-6, under “Results”).
It would have been obvious for one of ordinary skill in the art, at the time of filing, to combine the references of Pal et al. and Brubaker et al. Pal et al. teach a method for using gene expression data (paragraph [0141]) to determine biological pathways for potential drug targets for cancer (paragraphs [0162]-[0176]). Brubaker et al. teach that their DRIPP model can predict the response of a cell line with 80% accuracy and 88% precision (abstract). One of ordinary skill in the art would have been motivated to combine Pal et al. and Brubaker et al. to gain the benefit of increased accuracy and precision in predicting cell response. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success, because the model of Brubaker et al. may be readily included with the computations of Pal et al.
5. Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Pal et al. (US 2015/0269307) as applied to claims 1, 3, 5-13, and 15- 20 above, and further in view of Ionescu-Zanetti et al. (US 2017/0268037).
Pal et al. is applied as above.
Ionescu-Zanetti et al. teach isolating tumor cells comprise circulating tumor cells from the patient’s blood (paragraphs [0002] and [0058]).
It would have been obvious for one of ordinary skill in the art, at the time of filing, to combine the references of Pal et al. and Ionescu-Zanetti et al. Pal et al. teach a method for using gene expression data (paragraph [0141]) to determine biological pathways for potential drug targets for cancer (paragraphs [0162]-[0176]). Ionescu-Zanetti et al. teach enriching cells ins necessary for next generation sequencing (paragraph [0058]). One of ordinary skill in the art would have been motivated to combine Pal et al. and Ionescu-Zanetti et al. to gain the benefit of being able to identify biological pathways and gene expression data for circulating tumor cells using next generation sequencing. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success, because the method of Ionescu-Zanetti et al. may be used to gather data for the computations of Pal et al.
6. Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Pal et al. (US 2015/0269307) as applied to claims 1, 3, 5-13, and 15- 20 above, and further in view of Konantz et al. (“Zebrafish Xenografts as a Tool for in Vivo Studies on Human Cancer” Ann. N.Y. Acad. Sci. (2012) volume 1266, pages 124-137).
Pal et al. is applied as above.
Konantz et al. teach isolating tumor cells comprise circulating tumor cells from the patient’s blood (paragraphs [0002] and [0058]).
It would have been obvious for one of ordinary skill in the art, at the time of filing, to combine the references of Pal et al. and Konantz et al. Pal et al. teach a method for using gene expression data (paragraph [0141]) to determine biological pathways for potential drug targets for cancer (paragraphs [0162]-[0176]). Konantz et al. teach zebrafish offer advantages as a model for human cancer (abstract). One of ordinary skill in the art would have been motivated to combine Pal et al. and Konantz et al. to gain the benefit of using a zebrafish model over a murine model. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success, because the zebrafish model of Konantz et al. may replace the murine model used in Pal et al.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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/JERRY LIN/Primary Examiner, Art Unit 1685
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