DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Response to Amendment
Applicant’s amendment and reply of 01/13/2026 is acknowledged. Regarding the Office action mailed 10/16/2025, the rejection of claim 18 under 35 USC 102(a)(1) over Ahuja (US 2017/0009303) is withdrawn in view of the amendment; Ahuja does not disclose TMSB10 or CLDN3. The rejection of claims 18-20 over Meister is maintained. Applicant’s arguments will be addressed following the rejection.
Claim Rejections - 35 USC § 102
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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 18-20 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Meister (Journal of Bioinformatics Research Studies 1(1):1, 2014), as evidenced by https://artyomovlab.wustl.edu/phantasus/.
Meister obtained samples from lung cancer patients, extracted RNA, and analyzed gene expression my microarray analysis; see Abstract and sections 2.1-2.3 of Materials and Methods. The data were deposited in the GEO database under accession number GSE33532; see section 2.4 of Materials and Methods. This data set constitutes a biomarker expression signature based on the detected expression levels of all biomarkers analyzed, including those specifically recited in the claims.
As evidenced by the online analysis tool at https://artyomovlab.wustl.edu/phantasus/, the data generated by Meister included expression data for TMSB10, ISG15, CLDN3 and IFI27:
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The data also included expression data for MDK:
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The data also included expression data for CSTB:
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The data also included all remaining biomarkers recited in new claim 21, with ONE exception:
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The last gene listed in claim 21, TAGLN2, is not listed in the data of Meister. While the examiner was able to find evidence that an updated annotation of the HG-U133 Plus 2.0 array1 used by Meister does include at least one probe for this gene:
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neither the gene name TAGLN2, nor the probe ID 200916_at, is present in Meister’s data file. Therefore, the data file of Meister, which represents the generated “signature”, does not include TAGLN2. Consequently, claim 21 is NOT subject to this rejection.
Claim(s) 18-21 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kadara (J Natl Cancer Inst 2014 Mar; 106(3):dju004.) as evidenced by https://artyomovlab.wustl.edu/phantasus/.
Kadara obtained samples from lung cancer patients, extracted RNA, and analyzed gene expression my microarray analysis; see Abstract and first two sections of Materials and Methods. The data were deposited in the GEO database under accession number GSE44077; see second section of Materials and Methods. This data set constitutes a biomarker expression signature based on the detected expression levels of all biomarkers analyzed, including those specifically recited in the claims.
As evidenced by the online analysis tool at https://artyomovlab.wustl.edu/phantasus/, the data generated by Kadara included expression data for all the genes recited in the claims:
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A representative data for TAGLN2 for one of the tumor samples is shown here:
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Note that Kadara used a different microarray (Affymetrix Human Gene 1.0 ST) than Meister (HG-U133 Plus 2.0), which explains why Kadara’s data included TAGLN2, while Meister’s did not.
Response to Arguments
Applicant's arguments filed 01/13/2026 have been fully considered but they are not persuasive. Applicant argues that Meister does not “describe or suggest the claimed specific set of genes as a State 2 biomarker set and generating, as a technical output, a single biomarker expression signature from expression values of the plurality of genes belonging to the set.” This argument is not persuasive because Meister’s data set, as shown in the rejection, includes expression data for all genes except for TAGLN2. This data therefore represents a signature meeting the limitations of claims 18-20. That Meister did not “name” the data a “State 2 biomarker expression signature” is irrelevant. As claim 21 requires the full list of genes, and TAGLN2 is not found in Meister’s data, Meister does not anticipate claim 21. Furthermore, the claims are not limited to a signature containing ONLY the recited genes. Therefore, while Meister’s data does include “comprehensively measuring expression of thousands of genes across the transcriptome”, this claim is not limited to a certain maximum number of genes in the recited “signature”. The claims only require that certain genes be present in the “signature”. For the same reasons, the new grounds of rejection over Kadara (whose data do include all genes recited in the claims) applies.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, GARY BENZION can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
1 Available at https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-annotation-files.html