Patent Application 18662594 - COMPOSITIONS AND METHODS FOR SCREENING SOLID

Title: COMPOSITIONS AND METHODS FOR SCREENING SOLID TUMORS

Application Information

Invention Title: COMPOSITIONS AND METHODS FOR SCREENING SOLID TUMORS
Application Number: 18662594
Submission Date: 2025-05-12T00:00:00.000Z
Effective Filing Date: 2024-05-13T00:00:00.000Z
Filing Date: 2024-05-13T00:00:00.000Z
Examiner Employee Number: 70681
Art Unit: 1682
Tech Center: 1600

Rejection Summary

102 Rejections: 0
103 Rejections: 3

Cited Patents

The following patents were cited in the rejection:

US 0031240🔗

Office Action Text

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 .
Election/Restrictions
2. Applicant’s election without traverse of Group I and the species of the primer pair of SEQ ID NO: 1 and 2 in the reply filed on 05 March 2025 is acknowledged.
Claim Status
3. Claims 1-20 are pending.
Claims 15-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-14 read on the elected invention and have been examined herein. Claim 3 has been examined to the extent that it reads on the elected species of the primer pair of SEQ ID NO: 1 and 2. Claim 3 encompasses the non-elected species of primer pairs other than the combination consisting of SEQ ID NO: 1 and 2. Prior to the allowance of claims, any non-elected subject matter which has not been rejoined with the elected subject matter will be required to be removed from the claims.
Specification
4. The use of the terms “SMRT™” sequencing and “Ion Xpress™” which are a trade name or a mark used in commerce, have been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
These are two examples of a trademark that are used in the specification. The specification should be reviewed for any additional trademarks or trade names and the terms should be accompanied by their generic terminology and capitalized or where appropriate accompanied by a proper symbol.

Claim Rejections - 35 USC § 112(b) - Indefiniteness
5. 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 10 and 11 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 11 is indefinite over the recitation of “the adapter sequence” because this phrase lacks proper antecedent basis. Claim 1, from which claim 11 depends does not refer to an adapter sequence.
Claims 10 and 11 contain the trademarks/trade names “SMRT™” sequencing and “Ion Xpress™” respectively. MPEP 2173.05 states “If the trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of the 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982).”The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a particular type of sequencing (claim 10) and a particular type of adapter (claim 11) and, accordingly, the identification/description is indefinite.

Claim Rejections - 35 USC § 112(a) – Written Description
6. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(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 the first paragraph of pre-AIA 35 U.S.C. 112:
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.

Claims 1-14 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. This is a Written Description rejection.
In analyzing the claims for compliance with the written description requirements of 35 U.S.C. 112, first paragraph, a determination is made as to whether the specification contains a written description sufficient to show they had possession of the full scope of their claimed invention at the time the application was filed.
For claims drawn to a genus, MPEP § 2163 states:
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021) ( "[T]he written description must lead a person of ordinary skill in the art to understand that the inventor possessed the entire scope of the claimed invention. Ariad, 598 F.3d at 1353–54 ('[T]he purpose of the written description requirement is to ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor's contribution to the field of art as described in the patent specification.' (internal quotation marks omitted).").”

MPEP § 2163 goes on to state:
“An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed. See, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004).”

Herein, the claims are drawn to methods for predicting the likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy in a HER-2 positive subject diagnosed as having breast cancer. The claims require “identifying the HER-2 positive subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, when a mutation in at least one of the amplicons corresponding to PIK3CA, PIK3R1 and PTEN is detected.”
The claims do not define the mutations in the PIK3CA, PIK3R1 or PTEN genes in terms of any specific structural properties. The claims encompass detecting any possible single or multiple nucleotide insertion, deletion or substitution in the 5’ or 3’ noncoding region or in any intron or exon of the recited genes or any translocation or rearrangement involving one or more of the PIK3CA, PIK3R1 and PTEN genes as indicative that a subject will lack responsiveness to treatment with an anti-HER-2 therapy.
The claims recite that the mutations are detected using primers to the genes. With respect to the elected subject matter, claim 3 recites that the primers are SEQ ID NO: 1 and 2, which amplify sequences in the PIK3CA gene. The specification does not teach where these primers hybridize in the PIK3CA gene and does not identify any particular mutations detected in the region amplified by these primers. Even with respect to the PIK3CA sequences amplified by SEQ ID NO: 1 and 2, the resulting amplicons may contain any undefined genetic alteration, including single and multiple nucleotide substitutions, deletions or insertions or may be part of an undefined translocation. The recited primer pairs are not allele specific primer pairs that amplify only particular mutations. Thus, the recitation of the primers of SEQ ID NO: 1 and 2 used to generate amplicons in the PIK3CA gene in claim 3 is not sufficient to establish that Applicant was in possession of a representative number of mutations in the PIK3CA gene, as well as in the additionally recited PTEN and PIK3R1 genes for which the primers are not defined.
With the exception of claim 2, the anti-HER-2 therapy is not defined in terms of any specific structural properties. Note that different mutations may be associated with responsiveness to different therapies and that the claims encompass a significantly large and diverse genus of anti-HER-2 therapies, which differ in their chemical structure and mechanism of action.
Further, claim 4 requires treating the Her-2 positive breast cancer subject with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected. Thus, claim 4 requires the detection of a mutation which is indicative that the subject should be treated with trastuzumab emtansine, rather than trastuzumab alone.
Thereby, the claims encompass assaying for a potentially very large genus of mutations, wherein mutations in any of the PIK3CA, PIK3R1 and PTEN genes are indicative of a lack of responsiveness of a HER-2 positive breast cancer subject to any of a diverse genus of anti-HER-2 therapies, or as indicative or responsiveness to trastuzumab emtansine (claim 4).
The specification does not disclose any particular mutations in the PIK3CA, PIK3R1 and PTEN genes of HER2-positive breast cancers which are correlated with a lack of responsiveness to anti-HER-2 therapies or a positive response to trastuzumab emtansine.
The specification does teach:
“Breast Cancer. 28 of the 30 breast cancer specimens were submitted for HER-2, ER, and PR testing. Of these, six (21%) were HER-2 positive and therefore likely candidates for trastuzumab treatment (FIG. 7 ). Although five of the six HER-2-positive cases showed no additional mutations in ERBB or P13K pathway genes, the solid tumor screening NGS assay of the present technology detected a PIK3CA mutation in one sample. This is significant because PIK3CA mutations in HER-2 positive tumors have been associated with lack of responsiveness to conventional anti-HER-2 therapies (e.g. trastuzumab and lapatinib). Berns et al., Cancer Cell 12:395-402 (2007). However, trastuzumab emtansine (Kadcyla, Genentech) may be efficacious in treatment of such tumors, since concurrent PIK3CA mutations do not appear to alter outcome with this alternate therapy (American Association for Cancer Research [AACR] 104th Annual Meeting: Abstract LB-63. Presented Apr. 8, 2013).”

Thus, the specification cites Berns et al as teaching PIK3CA mutations in HER-2 positive therapies that were correlated with lack of responsiveness to “conventional anti-HER-2 therapies (e.g. trastuzumab and lapatinib).” The specification notes that PIK3CA mutations were not correlated with responsiveness to the anti-HER-2 therapy of trastuzumab emtansine.
The cited Berns et al (2007) reference does teach detecting the PIK3CA activating mutations of H1047R, E542K and E545K mutations in breast tumor samples (p. 397, col. 1). However, Berns (p. 400, col. 1) states:
“In our analyses PTEN status or PIK3CA mutation status alone had only limited ability to predict prognosis after trastuzumab treatment (Figure 3A). However, combined analysis of PTEN status and PIK3CA status not only identified twice as many patients at increased risk for disease progression, but the combined analysis also reached statistical significance as a biomarker for prognosis after trastuzumab therapy (Figure 3C).”

The teachings of PIK3CA mutations in the Berns et al reference is not commensurate in scope with the broadly claimed genus of possible mutations in the PIK3CA, PIK3R1 and PTEN genes which are correlated with lack of responsiveness to anti-HER-2 therapy in HER-2 positive breast cancer.
The prior art of Xu (Breast Cancer Research. 2014. 16: 405; cited in the IDS) reports that the PIK3CA mutations of E542K, E545D/K and H1047R (and low PTEN expression) were not predictive of response of HER-2 positive breast cancer patients to treatment with the anti-HER-2 inhibitor of lapatinib (see abstract and p. 7, col. 2; see also p. 3, col 1, 3rd para in the section “Assay Methods”).
The prior art of Stern et al (Clinical Cancer Research. 01 May 2015. 21(9): 2065; cited in the IDS) reports that lack of PTEN expression was not correlated with / lack of responsiveness to trastuzumab treatment in HER2-positve breast cancers (p. 2070, col. 2).
It is acknowledged that the specification teaches the general methodology for sequencing and performing association studies. However, possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features. See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895.
Additionally, the specification does not disclose a clear structure-function relationship between the claimed genus of mutations and their association with lack of responsiveness to anti-HER-2 therapy in HER-2 positive breast cancer. No common structure has been disclosed to identify those members of the claimed genus of mutations which are associated with lack of responsiveness to anti-HER-2 therapy in HER-2 positive breast cancer. The structure of each mutation which has an effect on responsiveness to the anti-HER-2 therapy will vary depending on the identity of the gene and the location of the mutation in the gene, and is expected to also vary depending on the particular anti-HER2 therapy.
While the Federal Circuit has recognized that “the written description requirement can in some cases be satisfied by functional description,” it has made clear that “such functional description can be sufficient only if there is also a structure-function relationship known to those of ordinary skill in the art.” In re Wallach, 378 F.3d 1330, 1335 (Fed. Cir. 2004); see also, Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 964 (Fed. Cir. 2002) (holding that the written description requirement would be satisfied “if the functional characteristic of preferential binding . . . were coupled with a disclosed correlation between that function and a structure that is sufficiently known or disclosed”); Amgen Inc. v. Sanofi, 782 F.3d 1367, 1378 (Fed. Cir. 2017) (holding that an “adequate written description must contain enough information about the actual makeup of the claimed products”).
Herein, the claims recite a functional description of the claimed genus of mutations in the PIK3CA, PIK3R1 and PTEN genes but do not identify a correlation between the structure of the mutations and the claimed function of being indicative lack of responsiveness to anti-HER-2 therapy in HER-2 positive breast cancer.
With respect to the present invention, there is no record or description which would demonstrate conception of a representative number of mutations in the PIK3CA, PIK3R1 and PTEN genes that are indicative of lack of responsiveness to anti-HER-2 therapy in HER-2 positive breast cancer. Therefore, the claims fail to meet the written description requirement because the claims encompass a significantly large genus of mutations and PI3K/AKT/mTOR pathway inhibitors and second agents which are not described in the specification.
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.
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.

This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2 and 5-14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Behlke et al (PGPUB 2014/0031240; cited in the IDS) in view of Downing et al (WO 2012/092426; cited in the IDS), Basu et al (WO 2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809).
Behlke et al teaches a method for detecting at least one mutation in a plurality of cancer-related genes in a subject comprising: extracting genomic DNA from a formalin-fixed paraffin-embedded (FFPE) tumor sample obtained from a subject; generating a library comprising amplicons; and detecting at least one mutation in at least one of the plurality of amplicons using high throughput massively parallel sequencing (e.g., para [0030], [0057], [0076], [0247], [0308], [0316], [0318], [0326] and [9433]). Behlke teaches that the method is one that can be used to predict a patient’s response to treatment. Behlke teaches that the subject is one who has been diagnosed with breast cancer (see, e.g., para [0191], [0195], [0198], [0302], [0562] and [0564]). Behlke further teaches detecting the amplicons by performing massively parallel sequencing (e.g., para [0017], [0280] and [0433-0435]). It is also disclosed that the assay provides a multiplex analysis of the mutations in the cancer-related genes (e.g., para [0515]).
Behlke teaches that the method is one that detects mutations in one or more or all of the genes disclosed therein, which genes include each of the AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7, GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2, FGFR3, HRAS, MET, PTCHI, EGFR, FGFR4, IDH1, NOTCH1, and PTEN genes (see, e.g., para [0175-0176] and [0518] and Table 1A).
For example, Behlke (para [0174-0177] teaches sequencing genomic sequences from tumor samples to detect mutations in:
[0175] A) at least five, six, seven, eight, nine, ten, fifteen, twenty, twenty-five, thirty or more subgenomic intervals from a mutated or wild-type gene or gene product chosen from at least five or more of: ABL1, AKT1, AKT2, AKT3, ALK, APC, AR, BRAF, CCND1, CDK4, CDKN2A, CEBPA, CTNNB1, EGFR, ERBB2, ESR1, FGFR1, FGFR2, FGFR3, FLT3, HRAS, JAK2, KIT, KRAS, MAP2K1, MAP2K2, MET, MLL, MYC, NF1, NOTCH1, NPM1, NRAS, NTRK3, PDGFRA, PIK3CA, PIK3CG, PIK3R1, PTCH1, PTCH2, PTEN, RB1, RET, SMO, STK11, SUFU, or TP53;
[0176] B) at least five, six, seven, eight, nine, ten, fifteen, twenty, twenty-five, thirty, thirty-five, forty, forty-five, fifty, fifty-five, sixty, sixty-five, seventy, seventy-five, eighty, eighty-five, ninety, ninety-five, one hundred, one hundred and five, one hundred and ten, one hundred and fifteen, one hundred and twenty or more of subgenomic intervals from a mutated or wild type gene or gene product chosen from at least five or more of: ABL2, ARAF, ARFRP1, ARID1A, ATM, ATR, AURKA, AURKB, BAP1, BCL2, BCL2A1, BCL2L1, BCL2L2, BCL6, BRCA1, BRCA2, CBL, CARD11, CBL, CCND2, CCND3, CCNE1, CD79A, CD79B, CDH1, CDH2, CDH20, CDH5, CDK6, CDK8, CDKN2B, CDKN2C, CHEK1, CHEK2, CRKL, CRLF2, DNMT3A, DOT1L, EPHA3, EPHA5, EPHA6, EPHA7, EPHB1, EPHB4, EPHB6, ERBB3, ERBB4, ERG, ETV1, ETV4, ETV5, ETV6, EWSR1, EZH2, FANCA, FBXW7, FGFR4, FLT1, FLT4, FOXP4, GATA1, GNA11, GNAQ, GNAS, GPR124, GUCY1A2, HOXA3, HSP90AA1, IDH1, IDH2, IGF1R, IGF2R, IKBKE, IKZF1, INHBA, IRS2, JAK1, JAK3, JUN, KDM6A, KDR, LRP1B, LRP6, LTK, MAP2K4, MCL1, MDM2, MDM4, MEN1, MITF, MLH1, MPL, MRE11A, MSH2, MSH6, MTOR, MUTYH, MYCL1, MYCN, NF2, NKX2-1, NTRK1, NTRK2, PAK3, PAX5, PDGFRB, PKHD1, PLCG1, PRKDC, PTPN11, PTPRD, RAFT, RARA, RICTOR, RPTOR, RUNX1, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SOX10, SOX2, SRC, TBX22, TET2, TGFBR2, TMPRSS2, TNFAIP3, TNK, TNKS2, TOP1, TSC1, TSC2, USP9X, VHL, or WT1;
[0177] C) at least five, six, seven, eight, nine, ten, fifteen, twenty, or more subgenomic intervals from a gene or gene product according to Table 1, 1A, 2, 3 or 4;
Behlke teaches detecting the one or more alterations in the genes to predict responsiveness or lack of responsiveness to anti-cancer therapeutics (para [0237] and [0300] and Table 2).
The teachings of Behlke at para [0316] indicate that the method for detecting the at least one mutation in at least one of the panel of cancer-related genes in a tumor FFPE sample from a subject having cancer may be performed without using a bait set comprising nucleic acid sequences that are complementary to the plurality of amplicons. Further, the method of Behlke is one in which the library is generated without the quality of the genomic DNA extracted from the FFPE tumor sample being assessed by qPCR prior to generating the library.
Further, Downing teaches a method for detecting at least one mutation in a plurality of cancer-related genes in a subject comprising: extracting genomic DNA from a formalin-fixed paraffin-embedded (FFPE) tumor sample obtained from a subject; generating a library comprising amplicons; ligating an adaptor sequence to the ends of the plurality of amplicons and detecting at least one mutation in at least one of the plurality of amplicons using high throughput massively parallel sequencing (e.g., p. 1-2, 4, 31, 37, and 141-143). Downing makes clear that selecting a subset of amplicons in the library using a bait set is optional and need not be performed to effectively detect the at least one mutation.
That is, Downing states:
“in one aspect, the invention features a method of analyzing a tumor sample. The method comprises: (a) acquiring a library comprising a plurality of target members, e.g., tumor members, from a sample, e.g., a tumor sample;
(b) optionally, contacting the library with a bait set (or plurality of bait sets) to provide selected members (sometimes referred to herein as "library catch");
(c) acquiring a read for a subgenomic interval from a tumor member from said library or library catch, e.g., by sequencing, e.g., with a next generation sequencing method;
(d) aligning said read; and
(e) assigning a nucleotide value (e.g., calling a mutation, e.g., with a Bayeisan method) from said read for a preselected nucleotide position, e.g., for a preselected nucleotide position in each of a plurality of subgenomic intervals, e.g., each of a plurality genes,
thereby analyzing said sample,”
Downing then further states “In an embodiment, step (b) is absent” (p. 5).
Downing also teaches that the cancer-related genes to be assayed for a mutation include each of the AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7, GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2, FGFR3, HRAS, MET, PTCHI, EGFR, FGFR4, IDH1, NOTCH1, and PTEN genes (see, e.g., p. 25, 56, and Table 1A).
Further, the method of Downing is one in which the library is generated without the quality of the genomic DNA extracted from the FFPE tumor sample being assessed by qPCR prior to generating the library.
Downing states:
“Optimized methods and assays for sequencing large numbers of genes and gene products from samples, e.g., tumor samples, from one or more subjects by evaluating a selected group of genes and gene products are disclosed. In one embodiment, the methods and assays featured in the invention are used in a multiplex assay format, e.g., assays incorporated multiple signals from a large number of diverse genetic events in a large number of genes.”

According, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have generated a method of detecting at least one mutation in a plurality of cancer-related genes in a subject comprising: extracting genomic DNA from a formalin-fixed paraffin-embedded (FFPE) tumor sample obtained from a subject; generating a library comprising amplicons; and detecting at least one mutation in at least one of the plurality of amplicons using high throughput massively parallel sequencing, wherein the library is generated without using a bait set comprising nucleic acid sequences that are complementary to the plurality of amplicons and without the quality of the genomic DNA extracted from the FFPE tumor sample being assessed by qPCR prior to generating the library. One would have been motivated to have done so because the teachings of Behlke, particularly in combination with the teachings of Downing, suggest doing so in order to effectively detect mutations in well-known cancer-related genes as indicative of the responsiveness of a cancer to treatment.
Secondly, Behlke does not teach identifying the HER-2 positive subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, when a mutation in at least one of the amplicons corresponding to PIK3CA, PIK3R1 and PTEN is detected.
However, Behlke does teach detecting the PIK3CA H1047R mutation in breast cancer subjects as one of the “Approved/standard alterations that predict sensitivity or resistance to approved/standard therapies” (para [0528]; see also para [0534] and [0555-0556] and Table 1B.
Further, Basu et al teaches a method comprising: (a) extracting genomic DNA from a formalin fixed paraffin-embedded (FFPE) sample obtained from a subject having HER-2 positive breast cancer (e.g., para [0028], [0069], and [0108-0109]); (b) generating a library comprising amplicons comprising each of a plurality of cancer-related genes, said plurality of cancer-related genes comprising AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7,GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2,FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN (e.g., para [0200-0201], [0204], [0446]); (c) detecting at least one mutation in at least the PIK3CA amplicons; and (d) identifying the HER-2 positive subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, including trastuzumab therapy, when a mutation in at least one of the amplicons comprising PIK3CA gene sequences is detected (e.g., para [0070]; Table 25 at p. 217 and Table 26 at p. 224; and Figure 51).
Basu teaches that the mutations may be detected by pyrosequencing in a method that comprises “ ligating an adaptor nucleic acid to a nucleic acid under investigation and hybridizing the resulting nucleic acid to a bead; amplifying a nucleotide sequence in an emulsion; sorting beads using a picoliter multiwell solid support; and sequencing amplified nucleotide sequences by pyrosequencing methodology” (para [0207]).
At p. 217 (Table 25), Basu states “Evidence suggests that breast cancer patients with activation of the PI3K pathway due to PTEN loss or PIK3CA mutation/amplification have a significantly shorter survival following trastuzumab treatment.”
Additionally, Cizkova teaches that mutations in exons 9 and 20 of the PIK3CA gene are predictive of a significantly worse outcome of HER-2 positive breast cancer patients treated with the anti-HER2 therapy of trastuzumab as compared to HER-2 positive breast cancer patients having wildtype PIK3CA (see abstract and p. 1808 “RESULTS”).
In view of the teachings of Basu and Cizkova, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Behlke so as to have detected the presence of a mutation in the PIK3CA gene in the FFPE sample of a HER2 positive breast cancer patient as indicative of a lack of response to an anti-HER-2 therapy, and particularly trastuzumab therapy since Behlke teaches detecting PIK3CA mutations, such as H1047R in exon 20 or exon 9 mutations, in the FFPE samples to predict a breast cancer patient’s responsiveness to therapy and Basu teaches that mutations in the PIK3CA gene are predictive of a lack of responsiveness to trastuzumab therapy. One would have been motivated to have made such a modification of the method of Behlke in order to have achieved the advantage set forth by Behlke of selecting an appropriate therapy for the breast cancer subject.
Regarding claim 5, Basu teaches that the status of the breast cancer as being a HER2 positive breast cancer is determined by performing immunohistochemical (IHC) staining with antibodies or by FISH (e.g., para [0494-0495]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have further modified the method of Behlke so as to have included a step of determining that the breast cancer is HER-2 positive by performing IHC or FISH since Basu teaches that this is an effective means for identifying HER-2 positive breast cancer.
Regarding claims 6 and 11, Behlke teaches ligating an adapter sequence to the ends of the amplicons and teaches that the adaptor sequence may be a P5 or P7 adaptor (e.g., para [0017], [0247] and [0587-0588)).
Regarding claim 7, Behlke teaches that the library is generated using “less than 10ng” of genomic DNA extracted from the FFPE tumor sample (e.g., para [0316]).
Regarding claim 8, Behlke teaches that the library can be generated using less than 50ng or less than 10ng of genomic DNA extracted from the FFPE tumor sample (e.g., para [0316]), but does not specifically teach using 11-25 ng of the extracted genomic DNA from the FFPE tumor sample.
However, to have determined the quantity of extracted genomic DNA to be used in preparing the library would have been obvious and well-within the skill of the ordinary artisan. Behlke teaches that the methods disclosed therein can be performed using a small amount of DNA, particularly in those instances in which the amount of DNA available is limiting (€.g., para [0322]). The ordinary artisan would be well aware of the fact that a sufficient amount of genomic DNA would be required to generate a library containing a representative number of target nucleic acids available for amplification and sequencing. Thus, the ordinary artisan would have recognized the result-effective variable and would readily know how to assay for optimum quantity of genomic DNA to be used for generating the library. Accordingly, it would have been obvious to one of ordinary skill in the art and well-within the skill of the ordinary artisan before the effective filing date of the claimed invention to have determined the optimum quantity of extracted genomic DNA from the FFPE tumor samples, including 11-25 ng, and to have used this quantity in the step of generating a library in order to provide the most accurate and sensitive method for detecting the at least one mutation in the cancer-related genes.
Regarding claims 9 and 10, Behlke teaches that the mutations can be detected using massively parallel sequencing, such as SOLID sequencing or HeliScope single molecule sequencing (e.g., para [0433- 0435)).
Regarding claim 12, Behlke teaches attaching a barcode to the amplicons (e.g., para [0013]), which barcode is considered to be a unique index sequence.
Regarding claims 13 and14, Behlke does not teach detecting the at least one mutation in a heterogeneous FFPE tumor sample, particularly wherein 5% or 5-10% of the cells harbor the at least one mutation.
However, Downing exemplifies methods wherein tumor heterogeneity was detected in FFPE samples (p. 271-272). Downing also teaches that FFPE samples isolated from the margins of a hyperplastic colonic polyp, the KRAS p.G13D mutation was not detected in cells most distal to the polyp, but was detected in 4% of cells in the fifth most distal section, in 5% of the cells in the section closest to the polyp and in 6% of the cells isolated from a section from the edge of the polyp.
In view of the teachings of Downing that the method can be used to analyze heterogeneous tissue samples and can detect mutations in 5% of the cells of the sample, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have applied the method of detecting at least one mutation to FFPE samples from heterogeneous tumors, including tumors harboring 5% or 5-10% of a particular mutation, in order to have determined the heterogeneity of the tumor or cells in the sample and the frequency of the mutation in the sample.

8. Claim 3 is/are rejected under 35 U.S.C. 103 as being unpatentable over Behlke et al (PGPUB 2014/0031240; cited in the IDS) in view of Downing et al (WO 2012/092426; cited in the IDS), Basu et al (WO2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809), and further in view of NCBI Database GenBank Accession No. NG_012113.2 (National Library of Medicine. 04 May 2014, available via URL: < ncbi.nlm.nih.gov/nuccore/383087749?sat=18&satkey=13954163>; cited in the IDS), Samuels et al (U.S. Patent No. 8,026,053; cited in the IDS), Raymond, C. (U.S. 20120015821; cited in the IDS) and Mitsuhashi et al (Journal of Laboratory Analysis. 1996. 10: 285-293; cited in the IDS).
The teachings of Behlke, Downing, Basu and Cizkova are presented above.
The combined references do not teach performing the method to detect a mutation in the PIK3CA gene by performing a PCR amplification reaction with the primers of SEQ ID NO: 1 and 2.
However, as discussed above, Behlke does teach performing PCR to generate a library of amplicons prior to sequencing the amplicons to screen for the presence of a mutation in the amplicons, including PIK3CA amplicons (e.g., para [0318], [0322] and [0430]).
Further, the sequence of each of the genes in the set of genes disclosed by Behlke, including the PIK3CA gene, were known in the prior art. In particular, GenBank NG_012113.2 discloses the sequence of the PIK3CA gene. The sequences of present SEQ ID NO: 1 and 2 are both present in GenBank NG_012113.2.
In particular, the sequence of SEQ ID NO: 1 is present at nucleotides 55363-55385 of the PIK3CA gene in NG_012113.2

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The sequence of SEQ ID NO: 2 is present at nucleotides 55516-55535 of the PIK3CA gene in NG_012113.2

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Further, Samuels et al teaches methods for detecting PIKC3A mutations wherein the methods comprising amplifying PIKC3A nucleic acids using primer pairs to detect mutations in samples obtained from subjects having colorectal or breast cancer (e.g., col. 3, lines 19-44, col. 9-10 and Table 2). Samuels states “Primers for PCR amplification and sequencing were designed using the Primer 3 program” (col 21, line 35 to col. 22, line 1).
Samuels exemplifies a reverse primer (SEQ ID NO: 300 therein) which is 23 nucleotides in length and comprises the 20mer of present SEQ ID NO: 2 (as shown in the first alignment below).

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Samuels also teaches a forward primer (SEQ ID NO: 144 therein) that is 24 nucleotides in length and comprises the inverse complement of the 22mer of present SEQ ID NO: 4 (as shown in the alignment below):

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Raymond exemplifies primers for amplifying PIK3CA target nucleic acids, together with other target nucleic acids, to generate gene specific libraries (e.g., para [0016], [0111]). Raymond provides guidance for selecting primers to amplify PIK3CA nucleic acids (para [0115-0123] and states “selected using an exon primer selection software entitled “Exon Primer,” available on the UCSC Genome Bioinformatics browser” (para [0115]). In particular, Raymond discloses a primer (SEQ ID NO: 146 therein) that comprises present SEQ ID NO: 1:

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Moreover, the prior art provides extensive guidance, direction and motivation to select primers to amplify a target nucleic acid. For example, Mitsuhashi provides a review of the parameters which affect PCR sensitivity and specificity and discloses the parameters for the design of optimal PCR primer sequences. As stated in the abstract, “(I)n this review, all the requirements of PCR primers sequences are summarized, such as location, size of amplicon, length of primers, nucleotide composition, Tm, 3' terminal hybridization strength and frequency, hairpin formation energy, primer-to-primer specificity, and location of mismatches to sequences of cross-hybridization.” The teachings of Mitsuhashi indicate that it was well known in the art and well within the skill of the ordinary artisan to design PCR primers of optimum specificity for detecting target nucleic acids.
Designing primers which are equivalents to those taught in the art requires only routine experimentation. The parameters and objectives involved in the selection of primers were well known in the art at the time the invention was made. Software programs were readily available which aid in the identification of conserved and variable sequences and in the selection of optimum primer pairs. The prior art is replete with guidance and information necessary to permit the ordinary artisan to design additional primers for the amplification PIK3CA nucleic acids to screen for mutations in the PIK3CA gene, including primers consisting of SEQ ID NO: 1 and 2.
Given that the prior art teaches the complete sequence of the PIK3CA gene, provides the motivation to obtain primers to amplify known mutations in the PIK3CA gene, and provides extensive guidance as to how to select primers to known sequences to amplify target nucleic acids, it would have been obvious to one of ordinary skill in the art and well within the skill of the art at the time the invention was made to have generated primers for amplifying PIK3CA nucleic acids, including the primers of SEQ ID NO: 1 and 2, in order to have facilitated the detection of mutations in the PIK3CA gene. The ordinary artisan would have had more than a reasonable expectation of success of generating such primers given the extensive guidance provided in the prior art.
Note that the disclosure has not established any unexpected results obtained by performing the recited methods using the primers of SEQ ID NO: 1 and 2 and the claims do not require detecting any particular mutations.
For the reasons set forth above, the use of primers of SEQ ID NO: 1 and 2 in the modified method of Behlke to assay for mutations in the PIK3CA gene would have been obvious to one of ordinary skill in the art and well within the skill of the ordinary artisan. Note also that the claimed method may include generating additional amplicons because the claims recite the open claim language of “comprising” and thereby may include any additional steps and may amplify and/or detect mutations in any other genes.
9. Claim 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Behlke et al (PGPUB 2014/0031240; cited in the IDS) in view of Downing et al (WO 2012/092426; cited in the IDS), Basu et al (WO 2014/089241), and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809), and further in view of Baselga et al (Cancer Research. April 2013. 73 (8_Supplement) Abstract LB-63).
The teachings of Behlke, Downing, Basu and Cizkova are presented above. The combined references do not teach treating the Her-2 positive breast cancer subject with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected.
However, Baselga teaches that activating mutations in PIK3CA may lead to resistance to HER2-targeted therapies. However, Baselga found that PIK3CA mutations did not affect the outcome of trastuzumab emtansine (T-DM1) treatment in HER2-positive metastatic breast cancer patients. Baselga states “T-DM1-treated pts with PIK3CA mutations had a similar treatment benefit as those without, suggesting that the unique mechanism of action of T-DM1 may overcome PIK3CA mutation resistance.”
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Behlke so as to have treated HER2-positive breast cancer subjects with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected. One would have been motivated to have done so because Baselga teaches that PIK3CA mutations do not affect the outcome of trastuzumab emtansine (T-DM1) treatment in HER2-positive metastatic breast cancer patients and thereby HER2-positive breast cancer subjects having PIK3CA mutations can be effectively treated with trastuzumab emtansine.
Double Patenting
10. 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 1-3 and 5-14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 10689710 (cited in the IDS) in view of Basu et al (WO 2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809).
It is acknowledged that the present application was filed as a divisional of U.S. application 16/870,033 which is a continuation of U.S. application 15/576,219 which issued as U.S. Patent No. 10689710. However, the subject matter of the present claims was not restricted from the claims which issued in ‘710. The prohibition against obviousness-type double patenting rejections under U.S.C. 121 only applies to divisional applications filed as a result of a restriction requirement. See MPEP 804.01.
The present claims and the claims of ‘710 are both inclusive of method for detecting at least one mutation in a plurality of cancer-related genes in a subject comprising: (a) extracting genomic DNA from a formalin fixed paraffin-embedded tumor sample obtained from the subject; (b) generating a library comprising amplicons corresponding to each of the plurality of cancer-related genes, said plurality of cancer-related genes comprising AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7, GNAQ, KRAS, PIK3CA, STKl1, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2, FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN, wherein (i) generating said library proceeds independently of using a bait set comprising nucleic acid sequences that are complementary to at least one of the plurality of amplicons; and (ii) the quality of the genomic DNA extracted from the formalin fixed paraffin-embedded tumor sample is not assessed using quantitative PCR prior to generating the library; (c) ligating an adapter sequence to the ends of the plurality of amplicons; and (d) detecting at least one mutation in at least one of the plurality of amplicons using high throughput massive parallel sequencing.
Regarding present claim 3, the claims of ‘710 also recite that the amplification reaction is performed using two primer pairs including the primers of SEQ ID NO: 1 and 2 (see claim 1 of ‘710).
The limitations of present claims 6-14 are recited in the dependent claims of ‘710.
The claims of ‘710 encompass methods wherein the subject has breast cancer (see claim 9). However, the claims of ‘710 do not recite that the subject has HER2-positive breast cancer and do not recite identifying the HER-2 positive breast cancer subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, when a mutation in at least one of the amplicons corresponding to PIK3CA, PIK3R1 and PTEN is detected.
However, Basu et al teaches a method comprising: (a) extracting genomic DNA from a formalin fixed paraffin-embedded (FFPE) sample obtained from a subject having HER-2 positive breast cancer (e.g., para [0028], [0069], and [0108-0109]); (b) generating a library comprising amplicons comprising each of a plurality of cancer-related genes, said plurality of cancer-related genes comprising AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7,GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2,FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN (e.g., para [0200-0201], [0204], [0446]); (c) detecting at least one mutation in at least the PIK3CA amplicons; and (d) identifying the HER-2 positive subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, including trastuzumab therapy, when a mutation in at least one of the amplicons comprising PIK3CA gene sequences is detected (e.g., para [0070]; Table 25 at p. 217 and Table 26 at p. 224; and Figure 51).
At p. 217 (Table 25), Basu states “Evidence suggests that breast cancer patients with activation of the PI3K pathway due to PTEN loss or PIK3CA mutation/amplification have a significantly shorter survival following trastuzumab treatment.”
Additionally, Cizkova teaches that mutations in exons 9 and 20 of the PIK3CA gene are predictive of a significantly worse outcome of HER-2 positive breast cancer patients treated with the anti-HER2 therapy of trastuzumab as compared to HER-2 positive breast cancer patients having wildtype PIK3CA (see abstract and p. 1808 “RESULTS”).
In view of the teachings of Basu and Cizkova, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method claimed in ‘710 so as to have detected the presence of a mutation in exon 9 or 20 of the PIK3CA gene in the FFPE sample of a HER2 positive breast cancer patient as indicative of a lack of response to an anti-HER-2 therapy, and particularly trastuzumab therapy, since Basu and Cizkova teach that mutations in exon 9 and 20 of the PIK3CA gene are predictive of a lack of responsiveness to trastuzumab therapy. One would have been motivated to have made such a modification of the method claimed in ‘710 in order to have achieved the advantage of selecting an appropriate therapy for HER-2 positive breast cancer subjects.
Regarding claim 5, Basu teaches that the status of the breast cancer as being a HER2 positive breast cancer is determined by performing immunohistochemical (IHC) staining with antibodies or by FISH (e.g., para [0494-0495]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have further modified the method claimed in ‘710 so as to have included a step of determining that the breast cancer is HER-2 positive by performing IHC or FISH since Basu teaches that this is an effective means for identifying HER-2 positive breast cancer.
11. Claim 4 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 10689710 in view of Basu et al (WO 2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809), and further in view of Baselga et al (Cancer Research. April 2013. 73 (8_Supplement) Abstract LB-63).
The claims of ‘710 and the teachings of Basu and Cizkova are presented above.
The claims of ‘710 do not recite treating the Her-2 positive breast cancer subject with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected.
However, Baselga teaches that activating mutations in PIK3CA may lead to resistance to HER2-targeted therapies. However, Baselga found that PIK3CA mutations did not affect the outcome of trastuzumab emtansine (T-DM1) treatment in HER2-positive metastatic breast cancer patients. Baselga states “T-DM1-treated pts with PIK3CA mutations had a similar treatment benefit as those without, suggesting that the unique mechanism of action of T-DM1 may overcome PIK3CA mutation resistance.”
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method claimed in ‘710 so as to have treated HER2-positive breast cancer subjects with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected. One would have been motivated to have done so because Baselga teaches that PIK3CA mutations do not affect the outcome of trastuzumab emtansine (T-DM1) treatment in HER2-positive metastatic breast cancer patients and thereby HER2-positive breast cancer subjects having PIK3CA mutations can be effectively treated with trastuzumab emtansine.
12. Claims 1-3, 5, 7-10 and 13-14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 and 9-11 of U.S. Patent No. 11981966 in view of Basu et al (WO 2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809).
It is acknowledged that the present application was filed as a divisional of U.S. application 16/870,033 which issued as U.S. Patent No. 11981966. However, the subject matter of the present claims was not restricted from the claims which issued in ‘966. The prohibition against obviousness-type double patenting rejections under U.S.C. 121 only applies to divisional applications filed as a result of a restriction requirement. See MPEP 804.01.
The present claims and the claims of ‘966 are both inclusive of a method for detecting at least one mutation in a plurality of cancer-related genes in a subject comprising: (a) extracting genomic DNA from a formalin fixed paraffin-embedded tumor sample obtained from the subject; (b) generating a library comprising amplicons corresponding to each of the plurality of cancer-related genes, said plurality of cancer-related genes comprising AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7, GNAQ, KRAS, PIK3CA, STKl1, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2, FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN, wherein (i) generating said library proceeds independently of using a bait set comprising nucleic acid sequences that are complementary to at least one of the plurality of amplicons; and (ii) the quality of the genomic DNA extracted from the formalin fixed paraffin-embedded tumor sample is not assessed using quantitative PCR prior to generating the library; and (c) detecting at least one mutation in at least one of the amplicons using high throughput massive parallel sequencing.
Regarding present claim 3, the claims of ‘966 also recite that the amplification reaction is performed using two primer pairs including the primers of SEQ ID NO: 1 and 2 (see claims 1 and 2 of ‘966).
The limitations of present claims 7-10, 13 and 14 are recited in dependent claims 5-7 and 9 of ‘966. Further regarding claim 10, when read in light of the specification of ‘966, it is clear that the recitation of massively parallel sequencing in claim 1 of ‘966 encompasses the methods set forth in present claim 10.
The claims of ‘966 encompass methods wherein the subject has breast cancer and at least one mutation is detected in an amplicon comprising PIK3CA, PIK3R1 or PTEN sequences (see claim 12 of ‘966). However, the claims of ‘966 do not recite that the subject has HER2-positive breast cancer and do not recite identifying the HER-2 positive breast cancer subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, when a mutation in at least one of the amplicons corresponding to PIK3CA, PIK3R1 or PTEN is detected.
However, Basu et al teaches a method comprising: (a) extracting genomic DNA from a formalin fixed paraffin-embedded (FFPE) sample obtained from a subject having HER-2 positive breast cancer (e.g., para [0028], [0069], and [0108-0109]); (b) generating a library comprising amplicons comprising each of a plurality of cancer-related genes, said plurality of cancer-related genes comprising AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7,GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2,FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN (e.g., para [0200-0201], [0204], [0446]); (c) detecting at least one mutation in at least the PIK3CA amplicons; and (d) identifying the HER-2 positive subject as having a likelihood of lack of responsiveness to treatment with an anti-HER-2 therapy, including trastuzumab therapy, when a mutation in at least one of the amplicons comprising PIK3CA gene sequences is detected (e.g., para [0070]; Table 25 at p. 217 and Table 26 at p. 224; and Figure 51).
At p. 217 (Table 25), Basu states “Evidence suggests that breast cancer patients with activation of the PI3K pathway due to PTEN loss or PIK3CA mutation/amplification have a significantly shorter survival following trastuzumab treatment.”
Additionally, Cizkova teaches that mutations in exons 9 and 20 of the PIK3CA gene are predictive of a significantly worse outcome of HER-2 positive breast cancer patients treated with the anti-HER2 therapy of trastuzumab as compared to HER-2 positive breast cancer patients having wildtype PIK3CA (see abstract and p. 1808 “RESULTS”).
In view of the teachings of Basu and Cizkova, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method claimed in ‘966 so as to have detected the presence of a mutation in exon 9 or 20 of the PIK3CA gene in the FFPE sample of a HER2 positive breast cancer patient as indicative of a lack of response to an anti-HER-2 therapy, and particularly trastuzumab therapy, since Basu and Cizkova teach that mutations in exon 9 and 20 of the PIK3CA gene are predictive of a lack of responsiveness to trastuzumab therapy. One would have been motivated to have made such a modification of the method claimed in ‘966 in order to have achieved the advantage of selecting an appropriate therapy for HER-2 positive breast cancer subjects.
Regarding claim 5, Basu teaches that the status of the breast cancer as being a HER2 positive breast cancer is determined by performing immunohistochemical (IHC) staining with antibodies or by FISH (e.g., para [0494-0495]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have further modified the method claimed in ‘966 so as to have included a step of determining that the breast cancer is HER-2 positive by performing IHC or FISH since Basu teaches that this is an effective means for identifying HER-2 positive breast cancer.
13. Claim 4 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 and 9-11 of U.S. Patent No. 11981966 in view of Basu et al (WO 2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809), and further in view of Baselga et al (Cancer Research. April 2013. 73 (8_Supplement) Abstract LB-63).
The claims of ‘966 and the teachings of Basu and Cizkova are presented above.
The claims of ‘966 do not recite treating the Her-2 positive breast cancer subject with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected.
However, Baselga teaches that activating mutations in PIK3CA may lead to resistance to HER2-targeted therapies. However, Baselga found that PIK3CA mutations did not affect the outcome of trastuzumab emtansine (T-DM1) treatment in HER2-positive metastatic breast cancer patients. Baselga states “T-DM1-treated pts with PIK3CA mutations had a similar treatment benefit as those without, suggesting that the unique mechanism of action of T-DM1 may overcome PIK3CA mutation resistance.”
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method claimed in ‘966 so as to have treated HER2-positive breast cancer subjects with trastuzumab emtansine when a mutation in an amplicon comprising PIK3CA sequences is detected. One would have been motivated to have done so because Baselga teaches that PIK3CA mutations do not affect the outcome of trastuzumab emtansine (T-DM1) treatment in HER2-positive metastatic breast cancer patients and thereby HER2-positive breast cancer subjects having PIK3CA mutations can be effectively treated with trastuzumab emtansine.
14. Claims 6,11 and 12 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 and 9-11 of U.S. Patent No. 11981966 in view of Basu et al (WO 2014/089241) and Cizkova et al (British Journal of Cancer. 2013. 108: 1807-1809), and further in view of over Behlke et al (PGPUB 2014/0031240; cited in the IDS).
The claims of ‘966 and the teachings of Basu and Cizkova are presented above.
Regarding claims 6 and 11, the claims of ‘966 do not recite ligating an adapter to the amplicons prior to sequencing the amplicons.
However, Behlke teaches ligating an adapter sequence to the ends of the amplicons and teaches that the adaptor sequence may be a P5 or P7 adapter / adaptor (e.g., para [0017], [0247] and [0587-0588)). It is disclosed that the ligation of an adapter sequence to the amplicons facilitates the subsequent sequencing of libraries of amplicons.
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method claimed in ‘966 so as to have included a step of ligating an adapter to the amplicons to facilitate the sequencing of the amplicons
Regarding claim 12, the claims of ‘966 do not recite attaching an index sequence to the amplicons.
However, Behlke teaches attaching a barcode to the amplicons (e.g., para [0013] and [0250]), which barcode is considered to be a unique index sequence. Behlke teaches that barcode sequences aid in the identification of amplicons present in a library when the library is sequenced (e.g., para [0013] and [0250]).
In view of the teachings of Behlke, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method claimed in ‘966 so as to have included a step of attaching a barcode / index sequence to the amplicons to achieve the benefit set forth by Behlke of aiding in the identification of the amplicons during the sequencing assay.
15. The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Li et al (Mol Diagn Ther. 30 April 2015. 19: 169-177 and Supplementary Tables 1-3) discloses methods to aid in selecting a treatment for patients having metastatic melanoma wherein the method comprises assaying a FFPE tumor sample from a patient to detect the presence of mutations associated with responsiveness of the tumor to therapy (see abstract). Li teaches that the method of screening for mutations comprises performing a next-generation sequencing assay to detect mutations in a panel of 34 cancer-associated genes (see abstract and “Discussion” at p. 175). The panel of 34 cancer-associated genes consists of the same genes as that recited in present claim 1 - i.e., the KT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7,GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2,FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN genes. See Supplementary Table 1.

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/CARLA J MYERS/Primary Examiner, Art Unit 1682