DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
1. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on June 18, 2025 has been entered.
Applicants’ arguments and amendments, filed June 18, 2025 have been fully considered and they are persuasive in-part. The following rejections are either reiterated or newly applied as necessitated by amendment. They constitute the complete set of rejections and/or objections presently being applied to the instant application.
Status of the Claims
Claims 38-45 are under examination.
Claim Rejections - 35 USC § 103
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 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 negated by the manner in which the invention was made.
3. Claims 38, 39, 42 and 43 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Ellis et al. (US 2009/0299640 A1) in view of Aziz et al. (WO 2008/082730 A2).
Instant claim 38 recite a step of assaying the cDNA to determine an expression level for a set of marker genes consisting of at least 10 and up to all of a listing of genes. While the transitional language of “consisting of” is closed language, the claim overall recites that the method is comprising additional steps to the step of assaying the cDNA. The MPEP §2111.03 (II) states, “However, the ‘consisting of’ phrase limits only the element set forth in that clause; other elements are not excluded from the claim as a whole.” In other words, the instant claims do not exclude the measurement of genes other than the listed marker genes.
In addition, claim 42 recites the transitional language of “consisting essentially of”. The MPEP §2111.03 (III) states, “For the purposes of searching for and applying prior art under 35 U.S.C. §102 and §103, absent a clear indication in the specification or claims of what the basic and novel characteristics actually are, "consisting essentially of" will be construed as equivalent to ‘comprising.’” Under the broadest reasonable interpretation, the instant claims would be interpreted as comprising the steps in claim 42.
Regarding claims 38 and 42, Ellis et al. teach a method for classifying or treating breast cancer (paragraph [0057] and [0069]) that includes obtaining a sample from a patient with prostate, bladder, brain, breast or lung cancer (paragraphs [0057] and [0201]); and determining the expression of CDCA8 (page 33, number 47), PRC1 (page 324, number 78).
However, Ellis et al. do not teach the amplifying 10-32 or up to all the markers of the panel of genes listed in the claim.
Aziz et al. teach a method that includes obtaining a tumor sample (page 309, lines 25-28) extracting RNA from a sample and reverse transcribing the RNA to cDNA (page 298, lines 17-31); assaying and amplifying the cDNA (page 300, lines 9-18) from a set of 10 or more genes from a panel of genes consisting of ASPM (page 49 #185), BIRC5 (page 44, #4), BUB1B (page 44, #11), C18orf24 (page 228 #6923), CDC2 (page 44 #16), CDC20 (page 44 #17), CDCA3 (page 205 #5896), CDCA8 (page 179 #4777), CDKN3 (page 58 #334), CENPF (page 44, #19), DTL (page 171 #4458), KIAA0101(page 47 #110), KIF20A (page 47 #113), KIF4A (page 48 #131), NUSAP1 (page 48 #149), ORC6L (page 156 #3817), PBK (page 185 #5032), PRC1 (page 47 #97), PTTG1 (page 47 #102), RAD54L (page 118 #2374), RRM2 (page 205 #469), and TOP2A (page 46 #83); and detecting the expression level of each gene in the set of marker genes (pages 300 and 301).
Regarding claims 39 and 43, Ellis et al. teaches normalizing the expression of the panel to the expression of housekeeping genes (paragraph [0063]).
It would have been obvious to one of ordinary skill in the art at the time of invention to combine the panel of Aziz et al. with the method of Ellis et al. Ellis et al. teach that classifying cancer requires identifying intrinsic genes of a subject to be used to classify a cancer (paragraph [0003[-[0007]. Aziz et al. provides a panels of genes that aid in classifying cancer (page 20). Thus, one of ordinary skill in the art would have been motivated to use the genes of Aziz et al.in the method of Ellis et al. to identify genes that can be used to classify cancer. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success, because both Aziz et al. and Ellis et al. use similar well known methods of measuring gene expression.
Response to Arguments
4. Applicants have amended the instant claims to recite “assaying the cDNA to determine an expression level for a set of marker genes consisting of at least 10 and up to all” of a listing of genes. However, as stated above, the instant claim recites “comprising” in the preamble which indicates that the claimed invention does not exclude additional steps. While Ellis et al. and Aziz et al. recite additional genes beyond what is recited in the claims, the instant claim does not exclude additional steps with additional genes. Thus, under the broadest reasonable interpretation, the combination of Ellis et al. and Aziz et al. fall within the scope of the instant claims.
Applicants also state that there is no motivation to arrive at that particular panel of genes. However, under the broadest reasonable interpretation, the “comprising” transitional language indicates that the claim as the whole does not exclude other genes. Thus, the motivation provided above is sufficient to make the claimed invention obvious over Aziz et al. and Ellis et al.
5. Claims 40 and 44 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Ellis et al. (US 2009/0299640 A1) in view of Aziz et al. (WO 2008/082730 A2) as applied to claims 38, 39, 42 and 43 above, and further in view of Kruse (US 2010/0324116 A1).
Ellis et al. and Aziz et al. are applied as above.
While Ellis et al. do teach normalizing gene expression levels to the expression level of housekeeping genes (paragraph [0063]), Ellis et al. and Aziz et al. do not teach where the housekeeping gene is RPL13A.
Regarding claims 11 and 31, Kruse teaches where normalizing gene expression levels of a panel of genes to housekeeping gene RPL13A (paragraph [0249]).
It would have been obvious to one of ordinary skill in the art at the time of invention to combine the methods of Ellis et al. and Aziz et al. with Kruse. The motivation to combine Ellis et al. and Aziz et al. is provided above. Kruse teaches a method of treating tumor cells (paragraph [0006] and [0079]). One of ordinary skill in the art would have been motivated to use the treatment methods of Kruse after using the diagnostic and prognostic methods of Ellis et al. to better treat the patient. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success in combining these methods, because one of ordinary skill could readily substitute the housekeeping genes of Ellis et al. with the housekeeping gene of Kruse.
Response to Arguments
6. This rejection is maintained for the reasons above.
7. Claims 41 and 45 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Ellis et al. (US 2009/0299640 A1) in view of Aziz et al. (WO 2008/082730 A2) as applied to claims 38, 39, 42 and 43 above, and further in view of Lauss et al. (WO 2008/077165 A1).
Ellis et al. and Aziz et al. are applied as above.
While Aziz et al. teach a panel that includes KIAA0101 (page 47 #110); CDCA8 (page 179 #4777), PRC1 (page 47 #97), CDKN3 (page 58 #334), NUSAP1 (page 48 #149), CDC2 (page 44 #16), DTL (page 171 #4458), ASPM (page 49 #185).
Ellis et al. and Aziz et al. do not teach including TK1 and FOXM1.
Lauss et al. teach biomarkers for breast cancer includes FOXM1 (page 2, line 34) and TK1 (page 3, line 16).
It would have been obvious for one of ordinary skill in the art, at the time of the invention, to utilize the biomarkers of Lauss et al. in the method of Ellis et al. and Aziz et al. Ellis et al. teach a method of diagnosing and prognosing cancer (paragraph [0006]). Lauss et al. teach that their makers provide for a reliable and efficient cancer diagnostic and prognostic method (page 9, lines 5-11). One of ordinary skill in the art would have been motivated to use the markers of Lauss et al. in the method of Ellis et al. and Aziz et al. to increase reliability and efficiency for diagnosing or prognosing cancer. Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success, since one of ordinary skill in the art may readily substitute the markers of Lauss et al. in to the method of Ellis et al. and Aziz et al.
Response to Arguments
8. This rejection is maintained for the reasons above.
Withdrawn Rejections
9. Applicant’s arguments and amendments, filed June 18, 2025, with respect to the rejection made under 35 U.S.C. §101 have been fully considered and are persuasive. As amended, the instant claims do not recite a judicial exception. This rejection has been withdrawn.
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