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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 3/25/2025 has been entered.
Note
Please note that Khaleda Hasan is now the examiner of record.
Application Status
Amended claims filed 3/25/2025 were entered. Claims 2 and 4 are now cancelled and claim 1 amended to add “comprising colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer”, to limit the subject to “human”, to require all SEQ ID NOs: 1-450 in the plurality of specific target genomic regions.
Claims 1, 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 are currently pending.
Any rejection or objection not reiterated herein has been overcome by amendment. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05/24/2025 was considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is defective because the sequence listing file size in listed in kilobytes instead of bytes.
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Drawings
The drawings are objected to for the following reasons:
37 CFR 1.84 (u)(1) states “View numbers must be preceded by the abbreviation "FIG.”
In the current case, the view numbers for Figures 1A-16 are preceded by the abbreviation "Fig." instead of the abbreviation "FIG." in all capital letters.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code in paragraphs [00422] and [00442]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the terms DNBSEQ™ (in at least paragraphs 0074, 00140, 00210, 00399-00401, and 00407-00410), METHYLCODE™ (in paragraph 0033), and NEBNEXT® (in paragraph 0046), which are trade names or marks used in commerce, have been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
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.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1, lines 7-9 reciting the limitation “a plurality of specific target genomic regions nucleic acid sequences comprising SEQ ID NOs: 1-450” appears to contain a typographical/grammatical error.
Claim 1 has periods in “i.”, “ii.”, “iii.”, and “iv.”. MPEP 608.01(m) states, “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations.” The Office suggests using parentheses to delineate steps to overcome this objection.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claim 12 is 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 12 contains the trademark/trade name DNBSEQ™. Where a 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 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See 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 specific sequencing technique and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 112 – new rejection necessitate by amendment
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, 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new rejection necessitated by Applicant’s amendment to cancel claims 2 and 4 and to add “comprising colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer”, to limit the subject to “human”, to require all SEQ ID NOs: 1-450 in the plurality of specific target genomic regions.
Claim Interpretation
The method of claim 1 is directed to a method for predicting the presence of a cancer comprising colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer. The method comprising steps: (a) bisulfite treating cell free DNA (cfDNA), (b) using the bisulfite treated cfDNA to prepare, for a genome of the species of the test human subject, a first sequencing library for a plurality of specific target genomic regions nucleic acid sequences comprising SEQ ID NOs: 1-450, wherein the plurality of specific target genomic regions is captured by a set of DNA probes from the bisulfite treated cfDNA, and a second sequencing library, wherein the second sequencing library comprises the bisulfite treated cfDNA that fails to bind to the set of probes; (c) sequencing the first and second libraries, thereby producing a plurality of sequencing results, (d) analyzing the first and second sequencing results, and (e) responsive to inputting into a previously trained model each of the analyzed sequenced results, receiving as output from the model a categorical prediction. The claims are sufficiently broad so as to encompass determining in any biological sample comprising cfDNA methylation in any cell type, any tissue type, any organ, and a wide variety of possible cancers in a human subject by determining a level and difference “of a specific cfDNA” using a machine learning or artificial intelligence protocol. Applicant amended claim 1 to recite “cancer comprising colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer”. However, the broadest reasonable interpretation in light of the recitation of “comprising” still encompasses cancers beyond the types recited.
Steps d and e of the instant claims are directed to this machine learning protocol. The results from the sequencing are input into a computer program. Then, somehow an output of a result that shows the presence or absence if particular types of cancer. This input/output of a computer program is not sufficiently described. The claims require SEQ ID NOs: 1-450 in which probes bind in step b)i) but then in b)ii) it includes sequencing the cfDNA that does not bind to the probes. Then, this information is somehow able to predict the presence or absence of cancer. However, the specification does not sufficiently describe how this process is done.
Teachings of the Specification
The specification provides some teachings in regards to a second sequencing library for a genome of species of the test subject from a flow through of the first library. The specification teaches “In some embodiments, the disclosed cfDNA library relates to 450 regions (e.g., containing 18,000 CpG sites) carrying methylation characteristic variations of many recorded types of cancer… After locking nonspecific sequences, this cfDNA library is hybridized with a probe set to capture target sequence regions. Next, magnetic beads are used to retain the probes bound to target sequence regions, for example, Dynabead™ streptavidin (provided by Invitrogen, USA). Meanwhile, the remaining sequences that are not captured by magnetic beads (called the "flow through" fragment) are recovered to analyze other markers.” (Specification, [00240]). The specification further teaches “Library fragment for analysis of genome-wide variations: In some embodiments, the other cfDNA library fragment is recovered by hybridization with biotin-bound probes ( e.g. a biotin-bound P5/P7 probe assembly provided by Integrated DNA Technologies- IDT, USA). In some embodiments, the cfDNA library fragment is obtained by streptavidin-bound magnetic beads (Dynabeads® M-270 Streptavidin beads - Invitrogen) via this bead's biotin-streptavidin binding. In some embodiments, the cfDNA library fragment is then PCR amplified and purified. PCR amplification can be performed using various suitable polymerases enzymes such as but not limited to KaPa Hifi hotstart Polymerase enzyme (provided by Roche, Switzerland).” (Specification [00241] and [00242]).
Additionally, the specification provides teachings of methylation density analysis. The specification teaches “Methylation density analysis at 450 target sequence regions: in some embodiments, the sequencing data from the disclosed cfDNA library fragment comprises the promoter, the exons, the introns, and specific regions in the whole genome. In some embodiments, the disclosed SPOT-MAS test procedure comprises sequencing at a higher depth which increases the resolution to identify differences of methylation at the threshold level of at least 1%. Thus, the SPOT-MAS test procedure as provided herein improves sensitivity in detecting methyl changes that occur at early stages of cancer cell development” (Specification, [00245]). Additionally, the specification teaches “The methylation and determination of genome-wide methylation status of tumor are similar to the methylation at specific sites of genes associated with tumor growth. However, when investigating genome-wide methylation characteristics, many studies demonstrated that the methylation status tends to decrease in many different cancers. This tendency of methylation decrease facilitates the activation of oncogenes, especially in the early stages of tumorigenesis. Thus, when comparing the trend of genome-wide methylation in cancer patients with healthy people, the trend of methylation decrease in cancer patients has been observed. Harnessing this feature allows cancer to be identified at a very early stage.” (Specification, [00282]). However, it is not described how methylation densities or different probes are indicative of cancer. For example, colon cancer vs. breast cancer. There is no description within the Specification of how the results of sequencing can be used to predict the presence or absence of cancer.
Furthermore, the Specification at paragraph [00125] defines the term “parameter” as any coefficient or, similarly, any value of an internal or external element (e.g., a weight and/or a hyperparameter) in an algorithm, model, regressor, and/or classifier that can affect (e.g., modify, tailor, and/or adjust) one or more inputs, outputs, and/or functions in the algorithm, model, regressor and/or classifier. For example, in some embodiments, a parameter refers to any coefficient, weight, and/or hyperparameter that can be used to control, modify, tailor, and/or adjust the behavior, learning, and/or performance of an algorithm, model, regressor, and/or classifier. In some instances, a parameter is used to increase or decrease the influence of an input (e.g., a feature) to an algorithm, model, regressor, and/or classifier. As a nonlimiting example, in some embodiments, a parameter is used to increase or decrease the influence of a node (e.g., of a neural network), where the node includes one or more activation functions. Assignment of parameters to specific inputs, outputs, and/or functions is not limited to any one paradigm for a given algorithm, model, regressor, and/or classifier but can be used in any suitable algorithm, model, regressor, and/or classifier architecture for a desired performance. In some embodiments, a parameter has a fixed value.” The Specification describes three specific parameters in paragraphs [00314], [00321], [00330], [00422], [00430], and [00443], and another seven parameters in paragraph [00422] without specifying the at least 100 parameters recited in claim 37 would enable one skilled in the art to use the combination model.
Additionally, regarding the methylation densities and comparison to healthy subjects, the specification teaches “Sequencing data from 19 healthy subjects were randomly selected to determine the average number of reads for each bin. Variation of gene copy number in each bin was evaluated based on the "Z score" value using the following formula:” (Specification, [00324]). The specification also teaches “Collect 10 ml of blood from patients with ovarian, liver, bronchial, pancreatic, stomach, colorectal, lung or breast cancers that are considered at stage I to III before surgery. The blood sample was then processed to obtain plasma. cfDNA was extracted from plasma using the commercial QIAsymphony DSP Circulating DNA Kit (937556).” (Specification, [0015]). The specification further teaches “DNA from cancer tissue samples and normal human tissue samples were used from the Biochain biobank, DNA sample from the tissue was fragmented into DNA pieces with the size of about 150 nucleotides to simulate the size of cfDNA molecules using the Covaris system (which used physical force to fragment DNA).” (Specification [0031]). Additionally, the specification teaches “AMF fractions in each sequence region of interest were compared between cancerous and healthy tissue samples. The dataset of 160 cancer tissue samples and 40 healthy tissue samples from Biochain was used to select DNA regions with different AMF values between these 2 groups of samples.” (Specification, [0036]). Additionally, the specification teaches “anomalous cfDNA methylation can identified as hypermethylation or hypomethylation, both of which may be indicative of cancer status” (Specification, [00137]).
No teachings within the specification indicate what specific combinations of the SEQ ID NOs: 1-450 would indicate a specific cancer. Without description of which of hypo/hypermethylation in regards to these sequences, one of ordinary skill in the art would not have adequate description to interpret results. Amended claim 1 is directed to “consisting of five or more nucleic acid sequences selected from SEQ ID NOs: 1-450.” Pursuant to MPEP 2163, the specification does not describe a structure that is common to the genus of sequences that are differentially methylated in cancer. As cited above, the specification states a dataset of 160 cancer tissue samples and 40 healthy samples from Biochain was used, Additionally, the small sample size has the same effect on “site specific methylation densities” from the sequencing results. The amended claim 1 being directed to comprising all SEQ ID NOs: 1-450 does not solve this lack of written description issue due to the claim interpretation, discussed above, and the further discussion below. Additionally, the claimed invention is directed to a liquid biopsy sample and it is not well described as to whether this will detect the presence of all cancers or only the specific cancers recited in amended claim 1.
However, there is no specific guidance as to a protocol that would identify differences in a single specific DNA with the level of sensitivity and specificity that the claims set forth. To satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention at the time of filing. MPEP 2161.01. Here, the specification does not disclose the steps necessary and/or flow charts of particular guidance as to how to achieve the outcomes stated in the claims.
State of the Art
The state of the art surrounding “flow through” and DNA methylation profiles for specific cancers as compared to healthy samples does not aid in further describing what is meant by “a plurality of site specific methylation densities…” Espín-Pérez et al. (Peripheral blood DNA methylation profiles predict future development of B-cell Non-Hodgkin Lymphoma. Precis. Onc. 2022; cited in the PTO-892 mailed 1/31/2024) demonstrates that DNA methylation profiles associated with specific cancers are still an emerging line of study. Additionally, Espin-Perez et al. states “Subjects with higher risk scores showed higher regulatory T-cells, memory B-cells, but lower naïve T helper lymphocytes fractions in the blood. Future prospective studies will be required to confirm the utility of our signature for managing patients who are at high risk for developing future NHL.” (Espin-Perez, Abstract). Additionally, Espin-Perez et al. teaches “Blood samples from a large population of healthy volunteers were taken and frozen using liquid nitrogen (1). Throughout a 16 years follow-up, subjects that developed NHL were registered (2). At the end of the follow-up, a balanced cohort comprising individuals that developed NHL and a matching ratio of controls was identified (3) and omics analyses were conducted on the selected frozen blood samples (4). Data was preprocessed and analyzed to develop a classifier for future NHL called Future LYmphoma Predictor or FLYP (5,6,7). Finally, the classifier was tested in a variety of independent NHL and healthy cohorts (8). BCLL = B-cell chronic lymphocytic leukemia, MM = multiple myeloma.” (Fig. 1, Workflow of the study). Therefore, the amendment of claim 1 to include SEQ ID NOs: 1-450 does not provide enough description on what a healthy subject profile would be in comparison to the cancerous profile. Especially in view of the claim interpretation, discussed above, regarding what is broadly encompassed and actually required of the specific targets or human subject profiles.
Wang et al. (DNA methylation profile in CpG-depleted regions uncovers a high-risk subtype of early-stage colorectal cancer. (2023) Journal of the National Cancer Institute; cited in the PTO-892 mailed 1/31/2024) teaches “The current risk stratification system defined by clinicopathological features does not identify the risk of recurrence in early-stage (stage I-II) colorectal cancer (CRC) with sufficient accuracy. We aimed to investigate whether DNA methylation could serve as a novel biomarker for predicting prognosis in early-stage CRC patients” (Abstract). Wang et al. teaches that DNA methylation profiles are still being studied in relation to different cancers (in this example colorectal cancer). Wang et al. aids in demonstrating that a healthy subject methylation profile and cancerous profiles were not a known quantity or concept in the art. Additionally, that the methylation profiles are still being studied.
Conclusion
In conclusion, claims 1, 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 are directed to a method for predicting the presence of a cancer, this method comprising additional steps involving building of multiple libraries and analysis of said libraries. In combination with the State of the Art, the teachings of the Specification, and general knowledge of the field of the art, “comprising SEQ ID NOs: 1-450, wherein the plurality of specific target genomics regions is captured by a set of DNA probes…” is not adequately described (in view of the claim interpretation discussed above). There is no guidance as to the finite sequence of steps for performing the task. There is no list of which parameters comprise the at least 100 parameters for the combination model. The specification amounts to an invitation to identify a protocol to accomplish the functions set out in the claim. It is not enough that one skilled in the art could write a program to achieve the claimed function because the specification must explain how the inventor intends to achieve the claimed function to satisfy the written description requirement, see MPEP 2161.01. Therefore, having considered all of this, it is concluded that applicant was not in possession of the claimed invention. The teachings of the Specification do not provide adequate description on building of sequencing libraries and the sequencing results, as well as site specific methylation densities. Additional information on “a plurality of site specific methylation densities” with comparisons of healthy vs cancerous subjects is required. Claims 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 suffer from the same inadequate written description problems as claim 1, as they depend from claim 1. Therefore, claims 1, 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 are rejected.
Response to Arguments
Applicant's arguments filed 3/25/2024 have been fully considered but they are not persuasive. The Examiner appreciates Applicant detailing on pages 9-16 in Remarks filed 3/25/2025 support for amendments in the specification. Applicant argues on pages 10-11 that the claimed machine learning protocol for predicting the presence of a cancer comprising colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer is fully supported by the written description of the specification. Applicant points to paragraphs [00335] - [00343] in the specification and reference Zeiler, 2012 "ADADELTA: an adaptive learning rate method”, and paragraph [00349] for support that after selecting useful attributes, a logistic regression machine learning algorithm was used to build a model using a training sample group to help determine the probability value of 5 cancer types of that sample and then, the organ origin of ctDNA was determined based on the highest probability value of that organ. These details still do not provide sufficient support on how results from the sequencing are inputted into a computer model and how the output results show the presence or absence of particular types of cancer, e.g., which parameters are adjusted and at what points during the combination model.
Applicant further argues that the novel and inventive features presently claimed rely mainly on the type of data, and how such data was acquired (liquid biopsy sample, SEQ ID Nos. 1-450, targeted sequencing, and 3 types of data from flow-through sequencing) and used to predict the claimed five specific cancer types, as well as the claimed structure of the model, all of which are fully supported in the present specification. However, amended claim 1 recites “cancer comprising colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer”. As discussed above, the broadest reasonable interpretation encompasses cancers beyond the types recited and is not sufficiently supported for all other types. Accordingly, the specification does not provide enough information on how methylation densities or different probes are indicative of a specific cancer.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KHALEDA B HASAN whose telephone number is (571)272-0239. The examiner can normally be reached IFP, Monday - Friday 7:30am-5pm.
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, Neil Hammell can be reached at (571) 270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KHALEDA B HASAN/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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