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 .
Application Status
This action is written in response to applicant’s correspondence received 12/17/2025. Claims 1, 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 are currently pending and examined herein.
Claim 1 has been amended to narrow the types of cancer to “colon cancer, liver cancer, lung cancer, breast cancer, or gastric cancer”, to require “nucleic acid sequences represented by SEQ ID NOs: 1-450”, to specify “cancer” specific target genomic regions, and to specify that a previously trained model is a “machine learning” model.
Claims 1, 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 were previously rejected under 35 U.S.C. 112(a), first paragraph, as failing to comply with the written description requirement. Applicant’s arguments, see pages 3-12, filed 12/17/2025, with respect to claims have been fully considered and are persuasive. Applicant argues that by reading the written description provided in the specification (e.g. at paragraphs [00335] - [00350]), a person skilled in the art will readily understand the basis of the trained machine learning model that performs prediction of a presence or absence of specific types of cancer based on the claimed combination of results of four investigations, that the types of cancer are now limited to those described and predicted in Example 3 (and Figure 16). Applicant further argues that one skilled in the art would readily understand the claimed learning model with the description in paragraphs 0279-0297 of the instant specification (pages 7-9). The rejection of 10/1/2025 has been withdrawn in view of Applicant’s amendments to claim 1 and persuasive arguments.
However, upon further consideration, the Office has issued a new rejection under 101 (detailed below).
Note: There are amendments to claim 1 that are not marked up. In currently amended claim 1, A comma was added after "genomic regions" in line 8 and the word “and” has been deleted in line 10.
Specification - withdrawn
Objections to the specification are withdrawn in view of Applicant’s amendment to amend the incorporation by reference statement from the file size listed in kilobytes to bytes and to include proper symbols for trade names or marks used in commerce.
Specification - maintained
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code “www” 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.
Drawings - withdrawn
The drawings were received on 12/17/2025. These drawings are acceptable.
Claim Objections - withdrawn
The objection to claim 1 is withdrawn in view of Applicant’s amendments filed 12/17/2025 to correct a typographical error and to replace additional periods with parentheses in claim 1.
Claim Objections - withdrawn
Claim 1 is objected to because of the following informalities: there is an “and” missing in line 10 (which was present in the previous claim set filed 3/25/2025). Claim language throughout claim 1 refers to the “first and second” libraries. Amending the claim to add the word “and” with appropriate markings would be remedial. Appropriate correction is required.
Claim Rejections - 35 USC § 112 - withdrawn
Rejection of claim 12 is withdrawn in view of Applicant’s amendments filed 12/17/2025 to remove the trademark/name.
Claim Rejections - 35 USC § 112 – new rejections
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 1, 32, and 34 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 1 recites the limitation "the set of probes" in line 12. There is insufficient antecedent basis for this limitation in the claim. An amendment to “the set of DNA probes” would be remedial.
Claim 32 recites the limitation “the set DNA probes” in line 1. There is insufficient antecedent basis for this limitation in the claim. An amendment to “the set of DNA probes” would be remedial.
Claim 34 recites the limitation “the set of probes” in line 1. There is insufficient antecedent basis for this limitation in the claim. An amendment to “the set of DNA probes” would be remedial.
Claim Rejections - 35 USC § 101 – new rejection
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.
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. 101 because the claimed invention is directed to a law of nature and an abstract idea without significantly more.
Step 1: The claims satisfy Step 1 because they are directed to a process.
Step 2A – Prong 1: Claim 1 recites a method for predicting the presence of colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer in a test human subject, the method comprising: (a-b) using bisulfite treated cfDNA from the test human subject to prepare (i) a first sequencing library for a plurality of cancer specific target genomic regions, comprising nucleic acid sequences represented by SEQ ID NOs: 1-450, captured by a set of DNA probes from the bisulfite treated cfDNA, and (ii) a second sequencing library, comprising the bisulfite treated cfDNA that fails to bind to the set of probes; c) sequencing the prepared first and second sequencing libraries, thereby producing a corresponding first and second plurality of sequencing results; d) analyzing the corresponding first and second plurality of sequencing results by measuring: (i) a plurality of site specific methylation densities, using the first plurality of sequencing results, for the plurality of cancer specific target genomic regions of the test human subject; (ii) a methylation density for the genome using the second plurality of sequencing results of the test human subject; (iii) a respective copy number of cfDNA across the genome, using the second plurality of sequencing results, of the test human subject, and (iv) a fragment size pattern distribution of cfDNA across the genome using the second plurality of sequencing results of the test human subject; and e) responsive to inputting into a previously trained machine learning model each of the analyzed sequencing results from (d)(i)-(d)(iv), receiving as output from the previously trained machine learning model a categorical prediction of a presence or absence of colon cancer, liver cancer, lung cancer, breast cancer or gastric cancer in the test human subject, a categorical prediction of a presence or absence of liver cancer in the test human subject, wherein the previously trained machine learning model is a composite model comprising four attribute models and a combination model, and wherein: each respective attribute model in the four attribute models produces a respective categorical classification upon input of a different one of the analyzed sequencing results from (d)(i)-(d)(iv), and the combination model combines the respective categorical prediction of the presence or absence of cancer in the test human subject of each attribute model in the four attribute models by a weighted combination of the respective categorical indication of the four attribute models, which is a natural phenomenon and an abstract idea. The claim encompasses in step d) i-iv, mental steps of analyzing sequencing results and the law of nature of correlating gene sequences to cancer, analogous to Examples i., v., and xi. in MPEP 2106.04(b). Thus, the claimed method constitutes a judicial exception.
Step 2A – Prong 2: Claim 1 reads on the judicial exception of a law of nature and mental steps and/or math. The physical steps (a) through (c) of using bisulfite treated cell free DNA (cfDNA) to prepare the first and second sequence libraries for a plurality of cancer specific target genomic regions comprising nucleic acid sequences represented by SEQ ID NOs: 1-450 from DNA probes are mere data gathering steps.
Furthermore, the nucleic acids sequences of cancer specific target genomic regions are well-known (Li et al. 2016; cited in the 892).
In Myriad, the Supreme Court considered the patent eligibility of several claims directed to isolated DNA related to the human BRCA1 and BRCA2 cancer susceptibility genes. The Supreme Court held that certain of Myriad Genetics' claims to isolated DNA are not patent-eligible, because they read on isolated naturally-occurring DNA that is a "product of nature." The Court held that isolating a "gene from its surrounding genetic material is not an act of invention." The Supreme Court held that other claims are patent eligible, because they are limited to cDNA, which is a type of man-made DNA composition that is not naturally occurring. The Court held that "cDNA is not a 'product of nature' and is patent eligible under §101.”
Step 2B: Claim 1 does not recite additional elements that are sufficient to amount to significantly more than the judicial exception. The claim does not included additional elements beyond receiving results of a genomic sequencing of a test human subject and steps (a)-(c), where the active steps are routine laboratory steps that are well-known, conventional and routine (MPEP 2106.05(d) Examples i., ii., ii., v., vii., and viii,). There are no steps that integrate the judicial exception into a practical application because the claim amounts to a law of nature and mental steps and/or math of receiving sequencing results.
Regarding dependent claims 3, 6-7, 9-10, 12-14, 16, 18-19, 23, 26-28, 31-32, and 34 dare included in the rejection as they do not recite any additional elements beyond receiving results of sequencing that would overcome Steps 2A or 2B. Claims are directed to a law of nature and abstract ideas using data gathered by conventional methods in the art.
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.
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/KHALEDA B HASAN/Examiner, Art Unit 1636
/BRIAN WHITEMAN/Primary Examiner, Art Unit 1636
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