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 and Arguments
Claims 1-24 are pending.
Claims 13 and 20, drawn to a non-elected invention is not examined on the merits.
Claims 2, 3, 6, 7, 13, 19 and 20 have been amended.
Claims 21-24 have been added.
Claims 1-12, 14-19 and 21-24 are examined on the merits.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Withdrawn Objection
Claim Objection
4. Claim 6 is no longer objected to because the acronym accompanies the full-term cholangiocarcinoma on line 1, see Amendments to the Claims submitted June 17, 2026.
Withdrawn Grounds of Rejection
Claim Rejections - 35 USC § 112
The rejection of claims 1-5 and 19 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, cited in the first action on the merits (FAOM), segment a. 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn in light of the amendment to claims 2, 3, 7, 19 reciting “antigen-binding fragment”, see Amendments to the Claims submitted June 17, 2026. Moreover, the rejection of claims 1 and 11 cited in FAOM, segment b. as being indefinite is withdrawn.
Claim 1 reads on a method for assessing cholangiocarcinoma (CAA) comprising detection of level(s) of tissue inhibitor of metalloproteinase-1 (TIMP-1) and/or matrix metalloproteinase-2 (MMP2) in a patient sample and reference sample with antibodies or antigen-binding fragments and comparing the levels between the two samples, wherein an increased level of TIMP1 and/or presence of matrix metalloproteinase-2 (MMP2) is indicative of cholangiocarcinoma (CCA).
New and Maintained Grounds of Rejection
Claim Rejections - 35 USC § 112
6. The rejection of claims 8, 11, 12 and 16-18 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 is maintained and made.
b. Claims 11 and claims read on methods for assessing cholangiocarcinoma (CAA) comprising detection of level(s) of tissue inhibitor of metalloproteinase-1 (TIMP-1) and/or matrix metalloproteinase-2 (MMP2) in a patient sample and reference sample with antibodies or antigen-binding fragments and comparing the levels between the two samples, wherein an increased level of TIMP1 and/or presence of matrix metalloproteinase-2 (MMP2) is indicative of cholangiocarcinoma (CCA). However, it remains unclear how one of ordinary skill in the art is able to differentiate between cholangiocarcinoma (CCA) and hepatocellular carcinoma (HCC) given these two malignancies are noted as liver cancer they arise from different cells, are treated differently and characteristics.
Likewise, claim 8 reads on a method for assessing CAA comprising determining levels of TIMP1, step (a’) and MMP2, step (b’) in a patient sample into a statistical methodology to produce an output value indicative for CCA diagnosis or risk of developing CCA. However, it is not clear what the output value should be to clarify between a definitive CCA diagnosis or the risk of developing CCA.
Applicant argues the “[t]he specification provides extensive guidance on establishing an appropriate reference level...Moreover, the specification provides robust ROC curve analysis and AUC data demonstrating the diagnostic performance of TIMP1 alone (AUC 0.939 for CCA vs. at-risk controls; AUC 0.715 for CCA VS. HCC) and in combination with MMP2 (AUC 0.922-0.977), providing a PHOSITA with a well-defined and reproducible framework for determining the discriminating level and output value in any given clinical context…A PHOSITA, armed with the specification's guidance on percentile-based cut-offs, ROC curve methodology, and logistic regression modeling, would have no difficulty determining the appropriate discriminating level and output value with reasonable certainty, consistent with the standard under Nautilus, 572 U.S. at 910.”, see the Remarks submitted June 17, 2026, page 11.
Applicant’s arguments and points of view have been carefully considered, but fail to persuade.
Claims should stand on their own. While Applicant points out passages within their specification cited herein and in the submitted Remarks “[i]t is improper to import claim limitations from the specification”, see MPEP 2111.01. While all of the technical details of a method need not be recited, the claim and/or dependent claims should include enough information to clearly and accurately describe the invention and how it is practiced. The method steps should at least include reagents necessary for the detection assay, wherein binding between reaction components is identified or visualized. However, the claims continue to not set forth clarity distinguishing how the methods yield discriminating information utilizing the measures other than diagnosis of cholangiocarcinoma. Accordingly, the metes and bounds cannot be determined and the rejection is maintained.
Claim Rejections - 35 USC § 101
7. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
8. The claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. Claim(s) 1-12 and 14-19 and new claims 21 and 22 is/are and continue to be directed to a judicial exception.
Applicant sets forth the legal standard and argues the claimed invention is “…[i]ntegrated into a [p]ractical [a]pplication and [i]nclude [s]ignificantly [m]ore [t]han [a]ny [j]udicial [e]xception”, see Remarks submitted June 17, 2026, segments A. and B. spanning 12-14. Applicant avers “[t]he independent claims recite a specific, ordered sequence of steps” and steps within the claimed invention “…[recite] a concrete diagnostic methodology that physically transforms a patient sample into clinically actionable diagnostic information-it is not a mental process or abstract idea. “, see paragraph (para.) spanning pages 13 and 14 of Remarks.
Applicant further avers “the claims do not merely observe a natural correlation” and “the claims are directed to a specific clinical context – the assessment of CCA,”, see page 14 of the Remarks, 1st full para.
Applicant asserts “the specification demonstrates that the claimed methods address a recognized unmet medical need identified by the EASL guidelines, providing direct and immediate clinical utility in enabling a physician to assess whether a patient has CCA, is at risk of developing CCA, or should be differentiated from HCC. See Specification, paras. [0013]-[0015], [0046]. This specific clinical workflow, directed toward a defined clinical output, integrates any judicial exception into a practical application.”, see Remarks, 1st full para.
Applicant argues the former Action fails to support the pending rejection and the anticipatory “…rejection further undermines any WURC assertion.”, see pages 15 and 16.
Applicant concludes arguments with a preemptive argument stating “[n]ew [c]laims 21-24 [p]atent [e]ligible”, see page 17 of the Remarks. The Examiner concurs with Applicant in regards to claims 23 and 24. However, claims 21 and 22 are not patent eligible.
Applicant’s arguments, points of view and Specification have been carefully considered, but fail to persuade.
The claimed invention is/continues to be directed to a law of nature without
significantly more. The claim(s) recite(s) the presence of TIMP1 in a patient sample greater than the reference level; presence of TIMP1 and MMP2 in a patient sample, as well as detection of patient’s level of one or both of the biomarkers with a binding molecule compared with a reference value is indicative of not only CCA, but also HCC, cirrhosis, chronic viral hepatitis, alcohol excess, toxins and a host of maladies cited in claim 12.
This relationship is a natural phenomenon that describes how the body naturally responds and expresses cancer biomarkers. This judicial exception is not integrated into a practical
application because the additional steps describing how the antibodies complex with one or both the biomarkers and the determined level is not an inventive step because the steps implemented to identify these complexes read on data gathering steps required to use the correlation and do not add a meaningful limitation to the method as they are insignificant extra-solution activity, step 2A, prong 2. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because at step 2B there is no inventive concept. Furthermore, the claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because sampling and measuring the level of antibodies against biomarkers and the quantification of the biomarkers, themselves is well
understood, routine and conventional in the art, hence “no” to Step 2B. Applicants’
specification provides what is known in the art regarding sampling and measuring, see
pages 22-34. There is no inventive concept.
Moreover, the claims contain mental processes and mathematical concepts, which are abstract ideas and a series of data gathering steps, level of biomarker(s) required to enter into a statistical methodology to produce an output value and may be performed in the mind. The statistical methodology requires variables, numbers and mathematical relationships for a computer-implemented system. This system is a tool to perform the mathematical concepts. While a process is not unpatentable simply because it contains a mathematical algorithm, the claims as a whole have been analyzed and determined to not contain additional elements or provide significantly more than the natural laws. The additional limitations such as observing signals of quantification and formed complexes between binding molecule(s) and biomarkers are insufficient to transform the identified natural law into a patentable process. Hence, the rejection is maintained and made for these reasons, those of record and herein.
Claims 1-12, 14-19 and new claims 21 and 22 are drawn to a non-statutory method having a "natural principle" as a limiting element or step without reciting additional elements/steps that integrate the natural principle into the claimed invention such that the natural principle is practically applied, and are sufficient to ensure that the claim amounts to significantly more than the natural principle itself.
In the instant case, the "natural principle" is: detection of level(s) of tissue inhibitor of metalloproteinase-1 (TIMP-1) and/or matrix metalloproteinase-2 (MMP2) in a patient sample and reference sample with antibodies or antigen-binding fragments and comparing levels between the two samples, wherein an increased level of TIMP1 and presence of matrix metalloproteinase-2 (MMP2) is indicative of cholangiocarcinoma (CCA) or suspected of having or has CCA, at risk of developing CCA and/or differentiates CCA from hepatocellular carcinoma (HCC).
The analysis as set forth in the 2019 Guidance is as follows:
Step 1: Yes, claims are drawn to a method which is one of the four statutory categories, a process.
Step 2A, prong 1: Yes, the claims recite/describe/set forth a judicial exception. The claims describe the relationship between the presence and/or level of TIMP2 and/or MMP2 in a patient’s sample is indicative of the patient has CCA, at risk of developing CCA and/or differentiates CCA from hepatocellular carcinoma (HCC).
Step 2A, prong 2: No, the judicial exception is not integrated into a practical application. The claims do not rely on or use the exception here. Once the presence and/or level of TIMP2 and/or MMP2 is detected in the patient’s sample by conventional means, i.e. implementing antibodies, there are no additional elements or combination of additional elements to apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
Step 2B: There is no inventive concept present in the clams. The steps of analyzing the presence of biomarker(s) or more specifically TIMP1 and/or MMP2 in a biological sample is established by well understood, routine conventional methods, i.e. data gathering necessary to perform the correlation. The claims and the steps within inform one of ordinary skilled in the art the level and/or presence of one or two biomarkers within a patient’s biological sample identifies an individual as affected with CCA, at risk of CCA, suspected of having or has CCC, and/or differentiates CCA from HCC. The claims do not recite additional elements that amount to significantly more than the judicial exception.
The claim(s) recite(s) detecting TIMP1 and/or MMP2 from a patient’s sample with antibodies to arrive at a CCA diagnosis. In regard to Step 2B, this judicial exception is not integrated into a practical application because the additional elements and do not add a meaningful limitation to the method because they amount to simply implementing the method using standard immunological techniques. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Moreover, the statistical methodology to produce an output value performed by a computing device and calculated level values and multivariate scores utilizing algorithms in the claims are regarded as abstract ideas. These are calculations implemented with a mathematical algorithm. These processes are not unpatentable simply because it contains a mathematical algorithm, the claims as a whole have been analyzed and determined to not contain additional elements or provide significantly more than the natural laws. Accordingly, these claims are not be eligible under step 2A or step 2B.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because assaying for candidate cancer biomarkers and making clinical decisions based on the presence of said biomarkers is routine in the art. This does not add significantly more and is not an inventive concept. Methods for making such determinations were well known in the art, these steps simply tell researchers to engage in well-understood, routine, conventional activity previously engaged in by scientists in the field. Such activities are normally not sufficient to transform an unpatentable law of nature into a patent-eligible application of such law. Detection of complexes comprising candidate cancer biomarkers and binding agents has been observed by applicant but not engineered by applicant. The claims do not add significantly more to the natural phenomenon because the claims do not require a novel reagent, apparatus of incorporate a novel treatment based on the correlation.
A claim that focuses on use of a natural principle must also include additional elements or steps to show that the inventor has practically applied, and added something significant to, the natural principle itself. See Mayo, 101 USPQ2d at 1966. Recited elements such as “determining”, “detecting”, “comparing”, “assessing”, “quantifying” and “providing” based on the natural principle impose no meaningful limit on the performance of the claimed invention. Likewise, as well as equations and formulas based on the natural principle impose no meaningful limit on the performance of the claimed invention.
As set forth the claims do not impose meaningful limits on the performance of the claimed invention.
Patents cannot be obtained on subject matter identified by the courts as being exempted from eligibility (i.e., laws of nature, natural phenomenon, and abstract ideas). Further, the active method steps are conventional and routine in the art for the reasons stated above and the claims do not amount to significantly more than the recited natural principle. The claims do not "practically apply" the natural principle; rather, the claims "simply inform" the natural principle to one performing routine active method steps and do not amount to significantly more than the natural principle itself. Thus, the technology used by the instant claims is well-known in the art and does not contribute significantly more to the judicial exception. See the 2019 Revised Patent Subject Matter Eligibility Guidance and Federal Register https://www.federalregister.gov/documents/2019/10/18/2019-22782/october-2019-patent-eligibility-guidance-update; and FDsys.gov.
Claim Rejections - 35 USC § 102
9. 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.
10. The rejection of claim(s) 1-5, 11, 12, 14, 15 and new claims 21-24 under 35 U.S.C. 102(a)(1) as being anticipated by Zhang et al., (Cancer Management and Research 10675-10681, published online 23 December 2019/ IDS reference #2 submitted March 14, 2025), as evidenced by Boster Biological Technology Co. Ltd. (Package insert, 11 pages and product info, 6 pages, printed February 2026) and IBM SPSS Statistics Base 17.0 User’s Guide [Computer software]. IBM Corp. 640 pages (2007) is maintained and made.
Applicant argues “Zhang does not disclose any method for assessing cholangiocarcinoma” and “…is directed exclusively to detecting MMP-2, MMP-9, TIMP-1, and TIMP-2 in the peripheral blood of patients with differentiated thyroid carcinoma (DTC) - specifically papillary and follicular thyroid carcinoma - and patients with benign thyroid lesions. See Zhang, Abstract; Introduction; Patients section. Zhang's patient population consists of 49 patients with benign thyroid lesions, 57 patients with DTC, and 20 healthy volunteers. Id., Patients section. Zhang contains no disclosure - express or inherent - of CCA, HCC, cholangiocarcinoma, hepatocellular carcinoma, bile duct, biliary tract, or any hepatobiliary cancer or disease context whatsoever.
The Office's characterization of Zhang as disclosing detection of TIMP-1 and MMP-2 indicative of cholangiocarcinoma (CCA) and distinguishing CCA from hepatocellular carcinoma (HCC) is factually incorrect and unsupported by the content of Zhang. Office Action, pp. 16-20. No such disclosure exists anywhere in Zhang. Accordingly, Zhang cannot anticipate the claimed methods, which are directed specifically to in vitro assessment of cholangiocarcinoma in a patient sample. See Claims 1 and 6.”, see Remarks submitted June 17, 2026, paragraphs (paras.) spanning pages 18 and 19.
Applicant’s arguments have been carefully considered, but fail to persuade.
Applicant’s claims read on a sample from any patient assayed for TIMP1, wherein the detected TIMP1 level within the patient’s sample is compared to a reference sample level of TIMP1. Based on the comparison between the two different samples, cholangiocarcinoma is diagnosed. An increased level of TIMP1 compared to the reference of TIMP1 is indicative the patient has cholangiocarcinoma.
Zhang anticipates the claims because it discloses detecting expression of TIMP-1 in serum utilizing a double sandwich ELISA method and comparing the results with the level in a control, healthy person, see page Figure 1 on page 10678. Hence, the rejection is maintained.
Zhang discloses detecting tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) in the peripheral blood and serum of cancer patients and healthy volunteers as a control group, see page 10676, Patients segment. The expression level of the biomarker was higher in cancer patients (particularly the preoperative patients) than the control, see Figure 1 on page 10678.
Figure 2 on page 10679 shows brighter bands of mRNA fragment of TIMP-1 from the preoperative cancer patients (lane 5) than the control group (lane 2), thereby reading on increased mRNA levels of the said biomarker. Therefore, both Figures evidence the detected levels are indicative for cholangiocarcinoma (CCA) and distinguishes CCA from hepatocellular carcinoma (HCC) and from risk of the additional disorders and diseases listed in claim 12.
The level of TIMP-1 in the serum of the cancer patients were detecting using the enzyme-linked immunosorbent assay (ELISA) method, see page 10676, 1st column (col.), lines 5-8; and Levels…segment on page 10676. “The expression of … TIMP-1 in the serum was detected using the double sandwich ELISA method according to the instructions provided by the manufacturer [Boster].”, see page 10676, 2nd col., lines 2-5.
As evidenced by Boster product info, “[t]he capture antibody is monoclonal antibody from mouse and the detection antibody is polyclonal antibody from goat.”, see page 2. Quantifiable signals are observed and calculated with the implementation of the biotinylated antibody, avidin-biotin-peroxidase (ABC) and substrate solution provided by Boster, see Boster product info, pages 2 and 3; and Boster package insert, page 2.
It is within the purview of the Examiner, differences in levels are “calculated” in the mind of the of the person of ordinary skill in the art when viewing the differences in brightness between the biomarker and the control, as well as viewing the ratio of levels noted in Figure 1 on page 10678. Notwithstanding, statistical analyses is performed on all data utilizing a computing device, see page 10676, 2nd col., Statistical Analyses segment. As evidenced by IBM SSPP…User’s guide the statistical methodology includes linear statistical models, quadratic model, discriminant analysis classification, nonparametric tests, logistic regression, clinical variables (gender, age), and multivariate models, see the entire guide and in particular, pages iii, 73, 120, 121, 164, 166, 174-176, 271, 275, 276, 280, 296, 300, 304, 307-308, 310, 320, 325, 326, 329, 343, 353, 359, 361, 368, 387, 390, 392-395, 398, 404, 422-440, 463, 465, 467 and 475.
11. The rejection of claim(s) 6-10, 16-19 and new claims 21-24 under 35 U.S.C. 102(a)(1) as being anticipated by Zhang et al., (Cancer Management and Research 10675-10681, published online 23 December 2019/ IDS reference #2 submitted March 14, 2025), as evidenced by Boster Biological Technology Co. Ltd. (Package insert, 11 pages and product info, 6 pages, printed February 2026) and IBM SPSS Statistics Base 17.0 User’s Guide [Computer software]. IBM Corp. 640 pages (2007) is maintained and made.
Applicant argues the basis of their arguments traversing the instant rejection is on the same basis as set forth previously, see Remarks submitted June 17, 2026, page 21, segment F.
Applicant’s arguments have been carefully considered, but fail to persuade.
Applicant’s claims read on a sample from any patient assayed for TIMP1, wherein the detected TIMP1 level within the patient’s sample is compared to a reference sample level of TIMP1. Based on the comparison between the two different samples, cholangiocarcinoma is diagnosed. An increased level of TIMP1 compared to the reference of TIMP1 is indicative the patient has cholangiocarcinoma.
Zhang anticipates the claims because it discloses detecting expression of TIMP-1 in serum utilizing a double sandwich ELISA method and comparing the results with the level in a control, healthy person, see page Figure 1 on page 10678. Hence, the rejection is maintained.
Zhang discloses detecting tissue inhibitor of matrix metalloproteinase-1 (TIMP-1) and matrix metalloproteinase-2 (MMP2) in the peripheral blood and serum of cancer patients and healthy volunteers as a control group, see page 10676, Patients segment. The expression levels of both biomarkers were higher than in the cancer patients (particularly the preoperative patients) than the control, see Figure 1 on page 10678.
Figure 2 on page 10679 shows brighter bands of mRNA fragment of MMP-2 and TIMP-1 from the preoperative cancer patients (lane 5) than the control group (lane 2), thereby reading on increased mRNA levels of the said biomarkers. Therefore, both Figures evidence the detected levels are indicative for cholangiocarcinoma (CCA) and distinguishes CCA from hepatocellular carcinoma (HCC) and from risk of the additional disorders and diseases listed in claim 12.
The levels of MMP-2 and TIMP-1 in the serum of the cancer patients were detecting using the enzyme-linked immunosorbent assay (ELISA) method, see page 10676, 1st column (col.), lines 5-8; and Levels…segment on page 10676. “The expression of MMP-1… and TIMP-1 in the serum was detected using the double sandwich ELISA method according to the instructions provided by the manufacturer [Boster].”, see page 10676, 2nd col., lines 2-5.
As evidenced by Boster product info, “[t]he capture antibody is monoclonal antibody from mouse and the detection antibody is polyclonal antibody from goat.”, see page 2. Quantifiable signals are observed and calculated with the implementation of the biotinylated antibody, avidin-biotin-peroxidase (ABC) and substrate solution provided by Boster, see Boster product info, pages 2 and 3; and Boster package insert, page 2.
It is within the purview of the Examiner, differences in levels are “calculated” in the mind of the of the person of ordinary skill in the art when viewing the differences in brightness between the biomarkers and the control, as well as viewing the ratio of levels noted in Figure 1 on page 10678. Notwithstanding, statistical analyses is performed on all data utilizing a computing device, see page 10676, 2nd col., Statistical Analyses segment. As evidenced by IBM SSPP…User’s guide the statistical methodology includes linear statistical models, quadratic model, discriminant analysis classification, nonparametric tests, logistic regression, clinical variables (gender, age), and multivariate models, see the entire guide and in particular, pages iii, 73, 120, 121, 164, 166, 174-176, 271, 275, 276, 280, 296, 300, 304, 307-308, 310, 320, 325, 326, 329, 343, 353, 359, 361, 368, 387, 390, 392-395, 398, 404, 422-440, 463, 465, 467 and 475.
Conclusion
12. 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.
13. Any inquiry concerning this communication or earlier communications from the Examiner should be directed to ALANA HARRIS DENT whose telephone number is (571)272-0831. The Examiner works a flexible schedule, however she can generally be reached 8AM-8PM, Monday through Friday.
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, Julie Wu can be reached at 571-272-5205. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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ALANA HARRIS DENT
Primary Examiner
Art Unit 1643
25 August 2026
/Alana Harris Dent/ Primary Examiner, Art Unit 1643
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